Mon Oct 16 22:48:11 EDT 2017 /HD4/Subjects/subj_23_1.long.s23_base /usr/local/freesurfer/bin/recon-all -long subj_23_1/ s23_base/ -all subjid subj_23_1.long.s23_base setenv SUBJECTS_DIR /HD4/Subjects FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux localhost.localdomain 3.10.0-327.3.1.el7.x86_64 #1 SMP Wed Dec 9 14:09:15 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 4096 maxlocks unlimited maxsignal 256758 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 65769812 2388068 59723144 21732 3658600 62994996 Swap: 12505084 0 12505084 ######################################## program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/17-02:48:12-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: mtobia Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-327.3.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/17-02:48:12-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: mtobia Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-327.3.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/17-02:48:12-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: mtobia Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-327.3.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/17-02:48:12-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: mtobia Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-327.3.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/17-02:48:12-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: mtobia Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-327.3.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/17-02:48:12-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: mtobia Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-327.3.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/17-02:48:12-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: mtobia Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-327.3.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/17-02:48:12-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: mtobia Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-327.3.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/17-02:48:12-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: mtobia Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-327.3.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/17-02:48:13-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: mtobia Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-327.3.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/17-02:48:13-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: mtobia Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-327.3.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/17-02:48:13-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: mtobia Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-327.3.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/17-02:48:13-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: mtobia Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-327.3.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/17-02:48:13-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: mtobia Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-327.3.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/17-02:48:13-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: mtobia Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-327.3.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/17-02:48:13-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: mtobia Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-327.3.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/17-02:48:13-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: mtobia Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-327.3.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/17-02:48:13-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: mtobia Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-327.3.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/17-02:48:13-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: mtobia Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-327.3.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/17-02:48:14-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: mtobia Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-327.3.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/17-02:48:14-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: mtobia Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-327.3.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/17-02:48:14-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: mtobia Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-327.3.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/17-02:48:14-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: mtobia Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-327.3.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/17-02:48:14-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: mtobia Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-327.3.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/17-02:48:14-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: mtobia Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-327.3.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/17-02:48:14-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: mtobia Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-327.3.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/17-02:48:14-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: mtobia Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-327.3.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/17-02:48:14-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: mtobia Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-327.3.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/17-02:48:14-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: mtobia Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-327.3.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/17-02:48:14-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: mtobia Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-327.3.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/17-02:48:15-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: mtobia Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-327.3.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/17-02:48:15-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: mtobia Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-327.3.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/17-02:48:15-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: mtobia Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-327.3.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/17-02:48:15-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: mtobia Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-327.3.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/17-02:48:15-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: mtobia Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-327.3.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/17-02:48:15-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: mtobia Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-327.3.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/17-02:48:15-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: mtobia Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-327.3.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/17-02:48:15-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: mtobia Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-327.3.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /usr/local/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #-------------------------------------------- #@# MotionCor Mon Oct 16 22:48:15 EDT 2017 mri_convert -at /HD4/Subjects/s23_base/mri/transforms/subj_23_1_to_s23_base.lta -odt uchar -rt cubic /HD4/Subjects/subj_23_1/mri/orig/001.mgz /HD4/Subjects/subj_23_1.long.s23_base/mri/orig.mgz mri_convert -at /HD4/Subjects/s23_base/mri/transforms/subj_23_1_to_s23_base.lta -odt uchar -rt cubic /HD4/Subjects/subj_23_1/mri/orig/001.mgz /HD4/Subjects/subj_23_1.long.s23_base/mri/orig.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /HD4/Subjects/subj_23_1/mri/orig/001.mgz... TR=2300.00, TE=2.98, TI=900.00, flip angle=9.00 i_ras = (-0.0437883, -0.999041, -2.37058e-08) j_ras = (-0.0922232, 0.0040422, -0.99573) k_ras = (-0.994775, 0.0436013, 0.0923117) INFO: Reading transformation from file /HD4/Subjects/s23_base/mri/transforms/subj_23_1_to_s23_base.lta... Reading transform with LTAreadEx() INFO: Applying transformation from file /HD4/Subjects/s23_base/mri/transforms/subj_23_1_to_s23_base.lta... --------------------------------- INFO: Transform Matrix (linear_ras_to_ras) 0.999 -0.025 -0.045 2.301; 0.028 0.998 0.061 5.135; 0.043 -0.062 0.997 20.091; 0.000 0.000 0.000 1.000; --------------------------------- Applying LTAtransformInterp (resample_type 5) MRItoBSpline degree 3 changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram writing to /HD4/Subjects/subj_23_1.long.s23_base/mri/orig.mgz... mri_convert -at /HD4/Subjects/s23_base/mri/transforms/subj_23_1_to_s23_base.lta -rt cubic /HD4/Subjects/subj_23_1/mri/orig/001.mgz /HD4/Subjects/subj_23_1.long.s23_base/mri/rawavg.mgz mri_convert -at /HD4/Subjects/s23_base/mri/transforms/subj_23_1_to_s23_base.lta -rt cubic /HD4/Subjects/subj_23_1/mri/orig/001.mgz /HD4/Subjects/subj_23_1.long.s23_base/mri/rawavg.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /HD4/Subjects/subj_23_1/mri/orig/001.mgz... TR=2300.00, TE=2.98, TI=900.00, flip angle=9.00 i_ras = (-0.0437883, -0.999041, -2.37058e-08) j_ras = (-0.0922232, 0.0040422, -0.99573) k_ras = (-0.994775, 0.0436013, 0.0923117) INFO: Reading transformation from file /HD4/Subjects/s23_base/mri/transforms/subj_23_1_to_s23_base.lta... Reading transform with LTAreadEx() INFO: Applying transformation from file /HD4/Subjects/s23_base/mri/transforms/subj_23_1_to_s23_base.lta... --------------------------------- INFO: Transform Matrix (linear_ras_to_ras) 0.999 -0.025 -0.045 2.301; 0.028 0.998 0.061 5.135; 0.043 -0.062 0.997 20.091; 0.000 0.000 0.000 1.000; --------------------------------- Applying LTAtransformInterp (resample_type 5) MRItoBSpline degree 3 writing to /HD4/Subjects/subj_23_1.long.s23_base/mri/rawavg.mgz... mri_add_xform_to_header -c /HD4/Subjects/subj_23_1.long.s23_base/mri/transforms/talairach.xfm /HD4/Subjects/subj_23_1.long.s23_base/mri/orig.mgz /HD4/Subjects/subj_23_1.long.s23_base/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Mon Oct 16 22:48:36 EDT 2017 /HD4/Subjects/subj_23_1.long.s23_base/mri cp /HD4/Subjects/s23_base/mri/transforms/talairach.xfm /HD4/Subjects/subj_23_1.long.s23_base/mri/transforms/talairach.auto.xfm cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Mon Oct 16 22:48:37 EDT 2017 /HD4/Subjects/subj_23_1.long.s23_base/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6179, pval=0.2817 >= threshold=0.0050) #-------------------------------------------- #@# Nu Intensity Correction Mon Oct 16 22:48:37 EDT 2017 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /HD4/Subjects/subj_23_1.long.s23_base/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ Linux localhost.localdomain 3.10.0-327.3.1.el7.x86_64 #1 SMP Wed Dec 9 14:09:15 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux Mon Oct 16 22:48:37 EDT 2017 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 tmpdir is ./tmp.mri_nu_correct.mni.6484 /HD4/Subjects/subj_23_1.long.s23_base/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.6484/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.6484/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig.mgz... TR=2300.00, TE=2.98, TI=900.00, flip angle=9.00 i_ras = (-1, 6.51926e-09, -2.23517e-08) j_ras = (-4.47035e-08, -8.73115e-10, -1) k_ras = (-4.65661e-10, 1, 2.03727e-10) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.6484/nu0.mnc... -------------------------------------------------------- Iteration 1 Mon Oct 16 22:48:39 EDT 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.6484/nu0.mnc ./tmp.mri_nu_correct.mni.6484/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.6484/0/ defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 165. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 170. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 211. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1051. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1054. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1449. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1455. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1457. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1481. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1631. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1633. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1635. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1637. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1639. (Maybe you should just omit the defined()?) [mtobia@localhost.localdomain:/HD4/Subjects/subj_23_1.long.s23_base/mri/] [2017-10-16 22:48:39] running: /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.6484/0/ ./tmp.mri_nu_correct.mni.6484/nu0.mnc ./tmp.mri_nu_correct.mni.6484/nu1.imp Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Number of iterations: 37 CV of field change: 0.000993305 [mtobia@localhost.localdomain:/HD4/Subjects/subj_23_1.long.s23_base/mri/] [2017-10-16 22:49:15] running: /usr/local/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.6484/nu0.mnc ./tmp.mri_nu_correct.mni.6484/0//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done -------------------------------------------------------- Iteration 2 Mon Oct 16 22:49:18 EDT 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.6484/nu1.mnc ./tmp.mri_nu_correct.mni.6484/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.6484/1/ defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 165. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 170. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 211. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1051. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1054. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1449. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1455. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1457. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1481. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1631. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1633. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1635. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1637. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1639. (Maybe you should just omit the defined()?) [mtobia@localhost.localdomain:/HD4/Subjects/subj_23_1.long.s23_base/mri/] [2017-10-16 22:49:18] running: /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.6484/1/ ./tmp.mri_nu_correct.mni.6484/nu1.mnc ./tmp.mri_nu_correct.mni.6484/nu2.imp Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Number of iterations: 22 CV of field change: 0.000963067 [mtobia@localhost.localdomain:/HD4/Subjects/subj_23_1.long.s23_base/mri/] [2017-10-16 22:49:33] running: /usr/local/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.6484/nu1.mnc ./tmp.mri_nu_correct.mni.6484/1//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.6484/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.6484/ones.mgz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /HD4/Subjects/subj_23_1.long.s23_base/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.6484/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.6484/ones.mgz sysname Linux hostname localhost.localdomain machine x86_64 user mtobia input ./tmp.mri_nu_correct.mni.6484/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.6484/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 Found 16777216 values in range Counting number of voxels Found 16777216 voxels in final mask mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.6484/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.6484/sum.junk --avgwf ./tmp.mri_nu_correct.mni.6484/input.mean.dat $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.6484/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.6484/sum.junk --avgwf ./tmp.mri_nu_correct.mni.6484/input.mean.dat sysname Linux hostname localhost.localdomain machine x86_64 user mtobia UseRobust 0 Loading ./tmp.mri_nu_correct.mni.6484/ones.mgz Loading orig.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 16777216.000 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.6484/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.6484/ones.mgz --i ./tmp.mri_nu_correct.mni.6484/nu2.mnc --sum ./tmp.mri_nu_correct.mni.6484/sum.junk --avgwf ./tmp.mri_nu_correct.mni.6484/output.mean.dat $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.6484/ones.mgz --i ./tmp.mri_nu_correct.mni.6484/nu2.mnc --sum ./tmp.mri_nu_correct.mni.6484/sum.junk --avgwf ./tmp.mri_nu_correct.mni.6484/output.mean.dat sysname Linux hostname localhost.localdomain machine x86_64 user mtobia UseRobust 0 Loading ./tmp.mri_nu_correct.mni.6484/ones.mgz Loading ./tmp.mri_nu_correct.mni.6484/nu2.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 16777216.000 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.6484/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.6484/nu2.mnc ./tmp.mri_nu_correct.mni.6484/nu2.mnc mul 1.02463792169248116997 Saving result to './tmp.mri_nu_correct.mni.6484/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.6484/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.6484/nu2.mnc nu.mgz --like orig.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.6484/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 6.51926e-09, -2.23517e-08) j_ras = (-4.47035e-08, -8.73115e-10, -1) k_ras = (-4.65661e-10, 1, 2.03727e-10) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 6 seconds. mapping ( 5, 116) to ( 3, 110) Mon Oct 16 22:50:02 EDT 2017 mri_nu_correct.mni done mri_add_xform_to_header -c /HD4/Subjects/subj_23_1.long.s23_base/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Mon Oct 16 22:50:03 EDT 2017 /HD4/Subjects/subj_23_1.long.s23_base/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 0.996 -0.046 -0.114 -3.914; 0.069 0.970 0.311 -50.804; 0.093 -0.321 1.037 15.800; 0.000 0.000 0.000 1.000; processing without aseg, no1d=0 MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 20 Starting OpenSpline(): npoints = 20 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 111 white matter peak found at 107 gm peak at 68 (68), valley at 42 (42) csf peak at 34, setting threshold to 56 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 67 (67), valley at 24 (24) csf peak at 33, setting threshold to 55 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 1 minutes and 52 seconds. #-------------------------------------------- #@# Skull Stripping Mon Oct 16 22:51:55 EDT 2017 /HD4/Subjects/subj_23_1.long.s23_base/mri cp -vf /HD4/Subjects/s23_base/mri/brainmask.mgz ./brainmask_s23_base.mgz '/HD4/Subjects/s23_base/mri/brainmask.mgz' -> './brainmask_s23_base.mgz' mri_mask -keep_mask_deletion_edits T1.mgz brainmask_s23_base.mgz brainmask.auto.mgz Transferring mask edits ('1' voxels) to dst vol DoAbs = 0 Writing masked volume to brainmask.auto.mgz...done. mri_mask -transfer 255 -keep_mask_deletion_edits brainmask.auto.mgz brainmask_s23_base.mgz brainmask.auto.mgz transfer mask voxels=255 to dst vol Transferring mask edits ('1' voxels) to dst vol DoAbs = 0 Writing masked volume to brainmask.auto.mgz...done. cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Mon Oct 16 22:52:00 EDT 2017 /HD4/Subjects/subj_23_1.long.s23_base/mri cp -vf /HD4/Subjects/s23_base/mri/transforms/talairach.lta transforms/talairach.lta '/HD4/Subjects/s23_base/mri/transforms/talairach.lta' -> 'transforms/talairach.lta' #-------------------------------------- #@# CA Normalize Mon Oct 16 22:52:00 EDT 2017 /HD4/Subjects/subj_23_1.long.s23_base/mri cp -vf /HD4/Subjects/s23_base/mri/aseg.mgz aseg_s23_base.mgz '/HD4/Subjects/s23_base/mri/aseg.mgz' -> 'aseg_s23_base.mgz' mri_ca_normalize -long aseg_s23_base.mgz -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta norm.mgz using longitudinal segmentation volume aseg_s23_base.mgz to generate control points... using MR volume brainmask.mgz to mask input volume... reading 1 input volume reading atlas from '/usr/local/freesurfer/average/RB_all_2008-03-26.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 102 --> 104 resetting gm mean[0]: 63 --> 63 input volume #1 is the most T1-like using real data threshold=24.0 skull bounding box = (58, 62, 51) --> (199, 210, 220) using (105, 111, 136) as brain centroid... mean wm in atlas = 104, using box (88,93,115) --> (122, 129,156) to find MRI wm before smoothing, mri peak at 106 after smoothing, mri peak at 106, scaling input intensities by 0.981 scaling channel 0 by 0.981132 using 244171 sample points... INFO: compute sample coordinates transform 0.993 -0.119 0.056 6.963; 0.080 1.071 0.350 -73.201; -0.090 -0.319 0.947 34.472; 0.000 0.000 0.000 1.000; INFO: transform used using 161941 total control points for intensity normalization... bias field = 0.993 +- 0.099 670 of 161941 control points discarded using 161941 total control points for intensity normalization... bias field = 1.002 +- 0.078 879 of 161941 control points discarded using 161941 total control points for intensity normalization... bias field = 1.003 +- 0.072 886 of 161941 control points discarded writing normalized volume to norm.mgz... freeing GCA...done. normalization took 1 minutes and 18 seconds. #-------------------------------------- #@# CA Reg Mon Oct 16 22:53:18 EDT 2017 /HD4/Subjects/subj_23_1.long.s23_base/mri mri_ca_register -nobigventricles -levels 2 -A 1 -l /HD4/Subjects/s23_base/mri/transforms/talairach.m3z identity.nofile -align-after -mask brainmask.mgz norm.mgz /usr/local/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.m3z not handling expanded ventricles... levels = 2 smoothing gradient with 1 averages... reading previously computed atlas xform /HD4/Subjects/s23_base/mri/transforms/talairach.m3z and applying inverse registration identity.nofile renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log ======= NUMBER OF OPENMP THREADS = 1 ======= reading input volume 'norm.mgz'... reading GCA '/usr/local/freesurfer/average/RB_all_2008-03-26.gca'... label assignment complete, 0 changed (0.00%) label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 **************** pass 1 of 1 ************************ setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.414, neg=0, invalid=96776 0001: dt=0.000050, rms=0.414 (0.074%), neg=0, invalid=96776 0002: dt=0.001750, rms=0.414 (0.001%), neg=0, invalid=96776 0003: dt=0.001750, rms=0.414 (0.001%), neg=0, invalid=96776 0004: dt=0.001750, rms=0.414 (0.001%), neg=0, invalid=96776 0005: dt=0.001750, rms=0.414 (0.001%), neg=0, invalid=96776 0006: dt=0.001750, rms=0.414 (0.001%), neg=0, invalid=96776 0007: dt=0.001750, rms=0.414 (0.003%), neg=0, invalid=96776 0008: dt=0.001750, rms=0.414 (0.002%), neg=0, invalid=96776 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.414, neg=0, invalid=96776 0009: dt=0.082051, rms=0.414 (0.032%), neg=0, invalid=96776 0010: dt=0.000094, rms=0.414 (-0.003%), neg=0, invalid=96776 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.407, neg=0, invalid=96776 0011: dt=0.001750, rms=0.407 (0.009%), neg=0, invalid=96776 0012: dt=0.001750, rms=0.407 (0.011%), neg=0, invalid=96776 0013: dt=0.007000, rms=0.407 (0.035%), neg=0, invalid=96776 0014: dt=0.000027, rms=0.407 (-0.003%), neg=0, invalid=96776 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.407, neg=0, invalid=96776 0015: dt=0.000109, rms=0.407 (0.000%), neg=0, invalid=96776 0016: dt=0.001750, rms=0.407 (0.012%), neg=0, invalid=96776 0017: dt=0.007000, rms=0.407 (0.048%), neg=0, invalid=96776 0018: dt=0.000438, rms=0.407 (0.007%), neg=0, invalid=96776 0019: dt=0.000438, rms=0.407 (0.003%), neg=0, invalid=96776 0020: dt=0.000438, rms=0.407 (0.005%), neg=0, invalid=96776 0021: dt=0.000438, rms=0.407 (0.007%), neg=0, invalid=96776 0022: dt=0.000438, rms=0.406 (0.007%), neg=0, invalid=96776 0023: dt=0.000438, rms=0.406 (0.010%), neg=0, invalid=96776 0024: dt=0.000438, rms=0.406 (0.013%), neg=0, invalid=96776 0025: dt=0.000438, rms=0.406 (0.013%), neg=0, invalid=96776 0026: dt=0.000438, rms=0.406 (0.015%), neg=0, invalid=96776 0027: dt=0.000438, rms=0.406 (0.018%), neg=0, invalid=96776 0028: dt=0.000438, rms=0.406 (0.016%), neg=0, invalid=96776 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.11725 (24) mri peak = 0.09500 (17) Left_Lateral_Ventricle (4): linear fit = 0.62 x + 0.0 (1952 voxels, overlap=0.173) Left_Lateral_Ventricle (4): linear fit = 0.62 x + 0.0 (1952 voxels, peak = 15), gca=14.8 gca peak = 0.14022 (22) mri peak = 0.09187 (17) Right_Lateral_Ventricle (43): linear fit = 0.68 x + 0.0 (1325 voxels, overlap=0.230) Right_Lateral_Ventricle (43): linear fit = 0.68 x + 0.0 (1325 voxels, peak = 15), gca=14.9 gca peak = 0.24234 (100) mri peak = 0.14610 (101) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (308 voxels, overlap=1.005) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (308 voxels, peak = 102), gca=102.5 gca peak = 0.19192 (97) mri peak = 0.12569 (110) Left_Pallidum (13): linear fit = 1.08 x + 0.0 (96 voxels, overlap=0.673) Left_Pallidum (13): linear fit = 1.08 x + 0.0 (96 voxels, peak = 104), gca=104.3 gca peak = 0.24007 (63) mri peak = 0.07091 (69) Right_Hippocampus (53): linear fit = 1.05 x + 0.0 (477 voxels, overlap=1.000) Right_Hippocampus (53): linear fit = 1.05 x + 0.0 (477 voxels, peak = 66), gca=66.5 gca peak = 0.29892 (64) mri peak = 0.09203 (67) Left_Hippocampus (17): linear fit = 1.01 x + 0.0 (486 voxels, overlap=0.993) Left_Hippocampus (17): linear fit = 1.01 x + 0.0 (486 voxels, peak = 65), gca=65.0 gca peak = 0.12541 (104) mri peak = 0.10745 (105) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (58098 voxels, overlap=0.858) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (58098 voxels, peak = 105), gca=104.5 gca peak = 0.13686 (104) mri peak = 0.09153 (107) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (52811 voxels, overlap=0.824) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (52811 voxels, peak = 106), gca=105.6 gca peak = 0.11691 (63) mri peak = 0.04603 (61) Left_Cerebral_Cortex (3): linear fit = 0.95 x + 0.0 (16389 voxels, overlap=0.945) Left_Cerebral_Cortex (3): linear fit = 0.95 x + 0.0 (16389 voxels, peak = 60), gca=60.2 gca peak = 0.13270 (63) mri peak = 0.04951 (58) Right_Cerebral_Cortex (42): linear fit = 0.94 x + 0.0 (16778 voxels, overlap=0.906) Right_Cerebral_Cortex (42): linear fit = 0.94 x + 0.0 (16778 voxels, peak = 59), gca=58.9 gca peak = 0.15182 (70) mri peak = 0.08454 (73) Right_Caudate (50): linear fit = 1.01 x + 0.0 (409 voxels, overlap=0.988) Right_Caudate (50): linear fit = 1.01 x + 0.0 (409 voxels, peak = 71), gca=71.0 gca peak = 0.14251 (76) mri peak = 0.10392 (77) Left_Caudate (11): linear fit = 0.98 x + 0.0 (509 voxels, overlap=0.967) Left_Caudate (11): linear fit = 0.98 x + 0.0 (509 voxels, peak = 74), gca=74.1 gca peak = 0.12116 (60) mri peak = 0.05294 (65) Left_Cerebellum_Cortex (8): linear fit = 1.08 x + 0.0 (10919 voxels, overlap=0.841) Left_Cerebellum_Cortex (8): linear fit = 1.08 x + 0.0 (10919 voxels, peak = 64), gca=64.5 gca peak = 0.12723 (61) mri peak = 0.05562 (65) Right_Cerebellum_Cortex (47): linear fit = 1.11 x + 0.0 (11990 voxels, overlap=0.859) Right_Cerebellum_Cortex (47): linear fit = 1.11 x + 0.0 (11990 voxels, peak = 67), gca=67.4 gca peak = 0.22684 (88) mri peak = 0.09315 (91) Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (6562 voxels, overlap=0.904) Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (6562 voxels, peak = 91), gca=91.1 gca peak = 0.21067 (87) mri peak = 0.09588 (88) Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (6214 voxels, overlap=0.923) Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (6214 voxels, peak = 88), gca=88.3 gca peak = 0.25455 (62) mri peak = 0.09350 (72) Left_Amygdala (18): linear fit = 1.09 x + 0.0 (311 voxels, overlap=1.010) Left_Amygdala (18): linear fit = 1.09 x + 0.0 (311 voxels, peak = 67), gca=67.3 gca peak = 0.39668 (62) mri peak = 0.08875 (64) Right_Amygdala (54): linear fit = 1.07 x + 0.0 (312 voxels, overlap=0.999) Right_Amygdala (54): linear fit = 1.07 x + 0.0 (312 voxels, peak = 66), gca=66.0 gca peak = 0.10129 (93) mri peak = 0.06299 (101) Left_Thalamus_Proper (10): linear fit = 1.03 x + 0.0 (3463 voxels, overlap=0.904) Left_Thalamus_Proper (10): linear fit = 1.03 x + 0.0 (3463 voxels, peak = 96), gca=96.3 gca peak = 0.12071 (89) mri peak = 0.05956 (90) Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (3334 voxels, overlap=0.920) Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (3334 voxels, peak = 90), gca=90.3 gca peak = 0.13716 (82) mri peak = 0.06482 (82) Left_Putamen (12): linear fit = 1.01 x + 0.0 (1371 voxels, overlap=0.999) Left_Putamen (12): linear fit = 1.01 x + 0.0 (1371 voxels, peak = 83), gca=83.2 gca peak = 0.15214 (84) mri peak = 0.05933 (78) Right_Putamen (51): linear fit = 0.96 x + 0.0 (1500 voxels, overlap=0.981) Right_Putamen (51): linear fit = 0.96 x + 0.0 (1500 voxels, peak = 81), gca=81.1 gca peak = 0.08983 (85) mri peak = 0.06616 (93) Brain_Stem (16): linear fit = 1.07 x + 0.0 (12587 voxels, overlap=0.778) Brain_Stem (16): linear fit = 1.07 x + 0.0 (12587 voxels, peak = 91), gca=90.5 gca peak = 0.11809 (92) mri peak = 0.07760 (97) Right_VentralDC (60): linear fit = 1.08 x + 0.0 (785 voxels, overlap=0.338) Right_VentralDC (60): linear fit = 1.08 x + 0.0 (785 voxels, peak = 99), gca=98.9 gca peak = 0.12914 (94) mri peak = 0.10425 (99) Left_VentralDC (28): linear fit = 1.04 x + 0.0 (887 voxels, overlap=0.611) Left_VentralDC (28): linear fit = 1.04 x + 0.0 (887 voxels, peak = 98), gca=98.2 gca peak = 0.21100 (36) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.13542 (27) mri peak = 0.19512 (19) gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.21802 (40) gca peak Third_Ventricle = 0.21100 (36) gca peak Fourth_Ventricle = 0.13542 (27) gca peak CSF = 0.17123 (45) gca peak Left_Accumbens_area = 0.25875 (69) gca peak Left_undetermined = 0.96240 (36) gca peak Left_vessel = 0.33262 (65) gca peak Left_choroid_plexus = 0.09846 (46) gca peak Right_Inf_Lat_Vent = 0.28113 (34) gca peak Right_Accumbens_area = 0.27120 (72) gca peak Right_vessel = 0.61915 (60) gca peak Right_choroid_plexus = 0.12775 (51) gca peak Fifth_Ventricle = 0.45329 (44) gca peak WM_hypointensities = 0.11729 (81) gca peak non_WM_hypointensities = 0.10912 (56) gca peak Optic_Chiasm = 0.33287 (75) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means estimating mean gm scale to be 1.02 x + 0.0 estimating mean wm scale to be 1.01 x + 0.0 estimating mean csf scale to be 0.64 x + 0.0 Left_Pallidum too bright - rescaling by 0.977 (from 1.075) to 101.9 (was 104.3) Right_Pallidum too bright - rescaling by 0.994 (from 1.025) to 101.9 (was 102.5) saving intensity scales to talairach.label_intensities.txt **************** pass 1 of 1 ************************ setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.407, neg=0, invalid=96776 0029: dt=0.007000, rms=0.407 (0.001%), neg=0, invalid=96776 0030: dt=0.005000, rms=0.407 (0.006%), neg=0, invalid=96776 0031: dt=0.001750, rms=0.407 (0.002%), neg=0, invalid=96776 0032: dt=0.000219, rms=0.407 (-0.000%), neg=0, invalid=96776 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.407, neg=0, invalid=96776 0033: dt=0.000200, rms=0.407 (0.000%), neg=0, invalid=96776 0034: dt=0.000438, rms=0.407 (0.001%), neg=0, invalid=96776 0035: dt=0.028000, rms=0.407 (0.038%), neg=0, invalid=96776 0036: dt=0.007000, rms=0.407 (0.015%), neg=0, invalid=96776 0037: dt=0.007000, rms=0.407 (0.011%), neg=0, invalid=96776 0038: dt=0.007000, rms=0.407 (0.019%), neg=0, invalid=96776 0039: dt=0.007000, rms=0.407 (0.010%), neg=0, invalid=96776 0040: dt=0.007000, rms=0.407 (0.009%), neg=0, invalid=96776 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.407, neg=0, invalid=96776 0041: dt=0.001250, rms=0.407 (0.007%), neg=0, invalid=96776 0042: dt=0.000000, rms=0.407 (0.000%), neg=0, invalid=96776 0043: dt=0.000049, rms=0.407 (-0.002%), neg=0, invalid=96776 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.407, neg=0, invalid=96776 0044: dt=0.000000, rms=0.407 (0.000%), neg=0, invalid=96776 label assignment complete, 0 changed (0.00%) ********************************************************************************************* ********************************************************************************************* ********************************************************************************************* ********************* ALLOWING NEGATIVE NODES IN DEFORMATION ******************************** ********************************************************************************************* ********************************************************************************************* ********************************************************************************************* **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.407, neg=0, invalid=96776 iter 0, gcam->neg = 2 after 200 iterations, nbhd size=1, neg = 2 starting rms=0.004, neg=2, removing folds in lattice.... iter 1, dt=0.000000: new neg 2, old_neg 2, delta 0, rms=0.004 (-0.000%) ---------- unfolding failed - restoring original position -------------------- 0045: dt=5.780000, rms=0.407 (0.000%), neg=0, invalid=96776 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.407, neg=0, invalid=96776 iter 0, gcam->neg = 2 after 200 iterations, nbhd size=1, neg = 2 starting rms=0.003, neg=2, removing folds in lattice.... iter 1, dt=0.000000: new neg 2, old_neg 2, delta 0, rms=0.003 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0046: dt=4.624000, rms=0.407 (0.000%), neg=0, invalid=96776 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.407, neg=0, invalid=96776 0047: dt=0.411765, rms=0.407 (0.009%), neg=0, invalid=96776 iter 0, gcam->neg = 28 after 200 iterations, nbhd size=3, neg = 23 starting rms=0.018, neg=23, removing folds in lattice.... iter 1, dt=0.000000: new neg 23, old_neg 23, delta 0, rms=0.018 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0048: dt=25.920000, rms=0.407 (-0.001%), neg=0, invalid=96776 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.407, neg=0, invalid=96776 iter 0, gcam->neg = 21 after 200 iterations, nbhd size=4, neg = 15 starting rms=0.010, neg=15, removing folds in lattice.... iter 1, dt=0.000000: new neg 15, old_neg 15, delta 0, rms=0.010 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0049: dt=36.288000, rms=0.407 (0.000%), neg=0, invalid=96776 label assignment complete, 0 changed (0.00%) label assignment complete, 0 changed (0.00%) ***************** morphing with label term set to 0 ******************************* **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.407, neg=0, invalid=96776 iter 0, gcam->neg = 13 after 200 iterations, nbhd size=4, neg = 9 starting rms=0.007, neg=9, removing folds in lattice.... iter 1, dt=0.000000: new neg 9, old_neg 9, delta 0, rms=0.007 (-0.000%) ---------- unfolding failed - restoring original position -------------------- 0050: dt=55.488000, rms=0.407 (-0.117%), neg=0, invalid=96776 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.407, neg=0, invalid=96776 iter 0, gcam->neg = 8 after 200 iterations, nbhd size=4, neg = 5 starting rms=0.003, neg=5, removing folds in lattice.... iter 1, dt=0.000000: new neg 5, old_neg 5, delta 0, rms=0.003 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0051: dt=110.976000, rms=0.407 (0.000%), neg=0, invalid=96776 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.407, neg=0, invalid=96776 iter 0, gcam->neg = 28 after 200 iterations, nbhd size=3, neg = 24 starting rms=0.018, neg=24, removing folds in lattice.... iter 1, dt=0.000000: new neg 24, old_neg 24, delta 0, rms=0.018 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0052: dt=25.920000, rms=0.407 (0.000%), neg=0, invalid=96776 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.407, neg=0, invalid=96776 iter 0, gcam->neg = 22 after 200 iterations, nbhd size=4, neg = 15 starting rms=0.010, neg=15, removing folds in lattice.... iter 1, dt=0.000000: new neg 15, old_neg 15, delta 0, rms=0.010 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0053: dt=36.288000, rms=0.407 (0.000%), neg=0, invalid=96776 writing output transformation to transforms/talairach.m3z... GCAMwrite registration took 0 hours, 25 minutes and 49 seconds. #-------------------------------------- #@# CA Reg Inv Mon Oct 16 23:19:07 EDT 2017 /HD4/Subjects/subj_23_1.long.s23_base/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z Inverting GCAM Saving inverse #-------------------------------------- #@# Remove Neck Mon Oct 16 23:19:51 EDT 2017 mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2008-03-26.gca nu_noneck.mgz erasing everything more than 25 mm from possible brain reading atlas '/usr/local/freesurfer/average/RB_all_2008-03-26.gca'... reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... removing structures at least 25 mm from brain... 10780171 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 0 minutes and 48 seconds. #-------------------------------------- #@# SkullLTA Mon Oct 16 23:20:39 EDT 2017 mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull_2.lta ======= NUMBER OF OPENMP THREADS = 1 ======= aligning to atlas containing skull, setting unknown_nbr_spacing = 5 using previously computed transform transforms/talairach.lta reading 1 input volumes... logging results to talairach_with_skull_2.log reading '/usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca'... average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu_noneck.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=6.0 skull bounding box = (43, 43, 37) --> (208, 237, 241) using (98, 108, 139) as brain centroid... mean wm in atlas = 126, using box (78,84,114) --> (118, 131,164) to find MRI wm before smoothing, mri peak at 104 after smoothing, mri peak at 105, scaling input intensities by 1.200 scaling channel 0 by 1.2 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.0, old_max_log_p =-3.9 (thresh=-3.9) 0.993 -0.119 0.056 6.963; 0.095 1.168 0.255 -75.180; -0.077 -0.155 0.991 5.917; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 1 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-4.0 (thresh=-4.0) 1.011 -0.121 0.057 4.819; 0.093 1.162 0.287 -78.351; -0.082 -0.197 1.001 10.638; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.029 -0.123 0.058 2.551; 0.092 1.177 0.326 -83.287; -0.085 -0.235 0.991 17.215; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 3 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.026 -0.131 0.047 5.883; 0.102 1.183 0.302 -83.669; -0.074 -0.207 0.998 11.813; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.026 -0.131 0.047 5.883; 0.102 1.183 0.302 -83.669; -0.074 -0.206 0.996 11.924; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3481 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.02568 -0.13051 0.04712 5.88307; 0.10211 1.18277 0.30198 -83.66862; -0.07374 -0.20643 0.99643 11.92355; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.02568 -0.13051 0.04712 5.88307; 0.10211 1.18277 0.30198 -83.66862; -0.07374 -0.20643 0.99643 11.92355; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 4 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 006: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.026 -0.131 0.047 5.883; 0.102 1.183 0.302 -83.669; -0.074 -0.206 0.996 11.924; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.9 (old=-3.9) transform before final EM align: 1.026 -0.131 0.047 5.883; 0.102 1.183 0.302 -83.669; -0.074 -0.206 0.996 11.924; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 382743 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.02568 -0.13051 0.04712 5.88307; 0.10211 1.18277 0.30198 -83.66862; -0.07374 -0.20643 0.99643 11.92355; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.02568 -0.13051 0.04712 5.88307; 0.10211 1.18277 0.30198 -83.66862; -0.07374 -0.20643 0.99643 11.92355; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 008: -log(p) = 4.3 tol 0.000000 final transform: 1.026 -0.131 0.047 5.883; 0.102 1.183 0.302 -83.669; -0.074 -0.206 0.996 11.924; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull_2.lta... registration took 16 minutes and 44 seconds. #-------------------------------------- #@# SubCort Seg Mon Oct 16 23:37:23 EDT 2017 /HD4/Subjects/subj_23_1.long.s23_base/mri cp -vf /HD4/Subjects/s23_base/mri/transforms/subj_23_1_to_s23_base.lta /HD4/Subjects/subj_23_1.long.s23_base/mri/transforms/subj_23_1_to_subj_23_1.long.s23_base.lta '/HD4/Subjects/s23_base/mri/transforms/subj_23_1_to_s23_base.lta' -> '/HD4/Subjects/subj_23_1.long.s23_base/mri/transforms/subj_23_1_to_subj_23_1.long.s23_base.lta' cp -vf /HD4/Subjects/s23_base/mri/transforms/subj_23_2_to_s23_base.lta /HD4/Subjects/subj_23_1.long.s23_base/mri/transforms/subj_23_2_to_subj_23_1.long.s23_base.lta '/HD4/Subjects/s23_base/mri/transforms/subj_23_2_to_s23_base.lta' -> '/HD4/Subjects/subj_23_1.long.s23_base/mri/transforms/subj_23_2_to_subj_23_1.long.s23_base.lta' cp -vf /HD4/Subjects/s23_base/mri/transforms/subj_23_3_to_s23_base.lta /HD4/Subjects/subj_23_1.long.s23_base/mri/transforms/subj_23_3_to_subj_23_1.long.s23_base.lta '/HD4/Subjects/s23_base/mri/transforms/subj_23_3_to_s23_base.lta' -> '/HD4/Subjects/subj_23_1.long.s23_base/mri/transforms/subj_23_3_to_subj_23_1.long.s23_base.lta' cp -vf /HD4/Subjects/s23_base/mri/transforms/subj_23_4_to_s23_base.lta /HD4/Subjects/subj_23_1.long.s23_base/mri/transforms/subj_23_4_to_subj_23_1.long.s23_base.lta '/HD4/Subjects/s23_base/mri/transforms/subj_23_4_to_s23_base.lta' -> '/HD4/Subjects/subj_23_1.long.s23_base/mri/transforms/subj_23_4_to_subj_23_1.long.s23_base.lta' mri_fuse_segmentations -a aseg.mgz -c aseg.auto_noCCseg.mgz -n norm.mgz subj_23_1.long.s23_base subj_23_1 subj_23_2 subj_23_3 subj_23_4 aseg.fused.mgz fusing took 0 minutes and 23 seconds. using aseg.mgz as aseg volume using aseg.auto_noCCseg.mgz as aseg no-CC-label volume using norm.mgz as norm volume reading /HD4/Subjects/subj_23_1.long.s23_base/mri/norm.mgz and processing 4 timepoints, writing to aseg.fused.mgz loading data for subject subj_23_1 ... loading data for subject subj_23_2 ... loading data for subject subj_23_3 ... loading data for subject subj_23_4 ... fusing... relabeled 18982 CC labels writing fused segmentation to aseg.fused.mgz mri_ca_label -align -r /HD4/Subjects/subj_23_1.long.s23_base/mri/aseg.fused.mgz -ri /HD4/Subjects/s23_base/mri/aseg.auto_noCCseg.label_intensities.txt norm.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz sysname Linux hostname localhost.localdomain machine x86_64 setenv SUBJECTS_DIR /HD4/Subjects cd /HD4/Subjects/subj_23_1.long.s23_base/mri mri_ca_label -align -r /HD4/Subjects/subj_23_1.long.s23_base/mri/aseg.fused.mgz -ri /HD4/Subjects/s23_base/mri/aseg.auto_noCCseg.label_intensities.txt norm.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 reading previously labeled volume from /HD4/Subjects/subj_23_1.long.s23_base/mri/aseg.fused.mgz... reading intensity scaling from /HD4/Subjects/s23_base/mri/aseg.auto_noCCseg.label_intensities.txt... reading 1 input volumes... reading classifier array from /usr/local/freesurfer/average/RB_all_2008-03-26.gca... reading input volume from norm.mgz... average std[0] = 6.9 reading transform from transforms/talairach.m3z... Atlas used for the 3D morph was /usr/local/freesurfer/average/RB_all_2008-03-26.gca reading label scales and offsets from /HD4/Subjects/s23_base/mri/aseg.auto_noCCseg.label_intensities.txt reading intensity scales from /HD4/Subjects/s23_base/mri/aseg.auto_noCCseg.label_intensities.txt label Left_Cerebral_Exterior (1): 0.60 + 0.0 label Left_Cerebral_White_Matter (2): 1.02 + 0.0 label Left_Cerebral_Cortex (3): 0.98 + 0.0 label Left_Lateral_Ventricle (4): 0.54 + 0.0 label Left_Inf_Lat_Vent (5): 1.01 + 0.0 label Left_Cerebellum_White_Matter (7): 1.03 + 0.0 label Left_Cerebellum_Cortex (8): 1.09 + 0.0 label Left_Thalamus (9): 1.01 + 0.0 label Left_Thalamus_Proper (10): 1.07 + 0.0 label Left_Caudate (11): 0.99 + 0.0 label Left_Putamen (12): 1.02 + 0.0 label Left_Pallidum (13): 1.04 + 0.0 label Third_Ventricle (14): 0.60 + 0.0 label Fourth_Ventricle (15): 0.60 + 0.0 label Brain_Stem (16): 1.06 + 0.0 label Left_Hippocampus (17): 1.01 + 0.0 label Left_Amygdala (18): 1.05 + 0.0 label CSF (24): 0.60 + 0.0 label Left_Accumbens_area (26): 0.99 + 0.0 label Left_VentralDC (28): 1.12 + 0.0 label Right_Cerebral_Exterior (40): 0.60 + 0.0 label Right_Cerebral_White_Matter (41): 1.02 + 0.0 label Right_Cerebral_Cortex (42): 0.96 + 0.0 label Right_Lateral_Ventricle (43): 0.66 + 0.0 label Right_Inf_Lat_Vent (44): 1.04 + 0.0 label Right_Cerebellum_White_Matter (46): 1.03 + 0.0 label Right_Cerebellum_Cortex (47): 1.11 + 0.0 label Right_Thalamus (48): 1.01 + 0.0 label Right_Thalamus_Proper (49): 1.05 + 0.0 label Right_Caudate (50): 1.03 + 0.0 label Right_Putamen (51): 0.98 + 0.0 label Right_Pallidum (52): 1.07 + 0.0 label Right_Hippocampus (53): 1.04 + 0.0 label Right_Amygdala (54): 1.00 + 0.0 label Right_Accumbens_area (58): 1.03 + 0.0 label Right_VentralDC (60): 1.12 + 0.0 label Fifth_Ventricle (72): 0.60 + 0.0 label (75): 0.00 + 0.0 label (76): 0.00 + 0.0 label WM_hypointensities (77): 1.02 + 0.0 label Left_WM_hypointensities (78): 1.02 + 0.0 label Right_WM_hypointensities (79): 1.02 + 0.0 label non_WM_hypointensities (80): 1.02 + 0.0 label Left_non_WM_hypointensities (81): 1.02 + 0.0 label Right_non_WM_hypointensities (82): 1.02 + 0.0 label (186): 0.00 + 0.0 label (187): 0.00 + 0.0 average std = 6.9 using min determinant for regularization = 4.7 0 singular and 0 ill-conditioned covariance matrices regularized pass 1: 87129 changed. image ll: -2.224, PF=1.000 pass 2: 20448 changed. image ll: -2.222, PF=1.000 pass 3: 4668 changed. writing labeled volume to aseg.auto_noCCseg.mgz... auto-labeling took 2 minutes and 29 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /HD4/Subjects/subj_23_1.long.s23_base/mri/transforms/cc_up.lta subj_23_1.long.s23_base will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /HD4/Subjects/subj_23_1.long.s23_base/mri/transforms/cc_up.lta reading aseg from /HD4/Subjects/subj_23_1.long.s23_base/mri/aseg.auto_noCCseg.mgz reading norm from /HD4/Subjects/subj_23_1.long.s23_base/mri/norm.mgz 94555 voxels in left wm, 209088 in right wm, xrange [104, 137] searching rotation angles z=[-0 14], y=[-4 10] searching scale 1 Z rot -0.1 searching scale 1 Z rot 0.1 searching scale 1 Z rot 0.4 searching scale 1 Z rot 0.6 searching scale 1 Z rot 0.9 searching scale 1 Z rot 1.1 searching scale 1 Z rot 1.4 searching scale 1 Z rot 1.6 searching scale 1 Z rot 1.9 searching scale 1 Z rot 2.1 searching scale 1 Z rot 2.4 searching scale 1 Z rot 2.6 searching scale 1 Z rot 2.9 searching scale 1 Z rot 3.1 searching scale 1 Z rot 3.4 searching scale 1 Z rot 3.6 searching scale 1 Z rot 3.9 searching scale 1 Z rot 4.1 searching scale 1 Z rot 4.4 searching scale 1 Z rot 4.6 searching scale 1 Z rot 4.9 searching scale 1 Z rot 5.1 searching scale 1 Z rot 5.4 searching scale 1 Z rot 5.6 searching scale 1 Z rot 5.9 searching scale 1 Z rot 6.1 searching scale 1 Z rot 6.4 searching scale 1 Z rot 6.6 searching scale 1 Z rot 6.9 searching scale 1 Z rot 7.1 searching scale 1 Z rot 7.4 searching scale 1 Z rot 7.6 searching scale 1 Z rot 7.9 searching scale 1 Z rot 8.1 searching scale 1 Z rot 8.4 searching scale 1 Z rot 8.6 searching scale 1 Z rot 8.9 searching scale 1 Z rot 9.1 searching scale 1 Z rot 9.4 searching scale 1 Z rot 9.6 searching scale 1 Z rot 9.9 searching scale 1 Z rot 10.1 searching scale 1 Z rot 10.4 searching scale 1 Z rot 10.6 searching scale 1 Z rot 10.9 searching scale 1 Z rot 11.1 searching scale 1 Z rot 11.4 searching scale 1 Z rot 11.6 searching scale 1 Z rot 11.9 searching scale 1 Z rot 12.1 searching scale 1 Z rot 12.4 searching scale 1 Z rot 12.6 searching scale 1 Z rot 12.9 searching scale 1 Z rot 13.1 searching scale 1 Z rot 13.4 searching scale 1 Z rot 13.6 global minimum found at slice 126.6, rotations (2.84, 6.88) final transformation (x=126.6, yr=2.839, zr=6.882): 0.992 -0.120 0.049 10.519; 0.120 0.993 0.006 -3.022; -0.050 0.000 0.999 15.416; 0.000 0.000 0.000 1.000; updating x range to be [125, 130] in xformed coordinates best xformed slice 128 cc center is found at 128 149 117 eigenvectors: -0.001 0.004 1.000; -0.200 -0.980 0.004; 0.980 -0.200 0.002; error in mid anterior detected - correcting... error in mid anterior detected - correcting... error in mid anterior detected - correcting... writing aseg with callosum to /HD4/Subjects/subj_23_1.long.s23_base/mri/aseg.auto.mgz... corpus callosum matter segmentation took 4.5 minutes #-------------------------------------- #@# Merge ASeg Mon Oct 16 23:44:42 EDT 2017 cp aseg.auto.mgz aseg.mgz #-------------------------------------------- #@# Intensity Normalization2 Mon Oct 16 23:44:42 EDT 2017 /HD4/Subjects/subj_23_1.long.s23_base/mri mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading from norm.mgz... Reading aseg aseg.mgz normalizing image... processing with aseg removing outliers in the aseg WM... 3585 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 111 white matter peak found at 109 gm peak at 68 (68), valley at 33 (33) csf peak at 11, setting threshold to 49 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 67 (67), valley at 33 (33) csf peak at 11, setting threshold to 48 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 2 minutes and 42 seconds. #-------------------------------------------- #@# Mask BFS Mon Oct 16 23:47:25 EDT 2017 /HD4/Subjects/subj_23_1.long.s23_base/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1783013 voxels in mask (pct= 10.63) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Mon Oct 16 23:47:27 EDT 2017 mri_segment brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (106.0): 106.6 +- 6.0 [80.0 --> 125.0] GM (70.0) : 69.0 +- 9.8 [30.0 --> 96.0] setting bottom of white matter range to 78.8 setting top of gray matter range to 88.6 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 13800 sparsely connected voxels removed... thickening thin strands.... 20 segments, 5292 filled 2222 bright non-wm voxels segmented. 8198 diagonally connected voxels added... white matter segmentation took 1.4 minutes writing output to wm.seg.mgz... mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.43 minutes reading wm segmentation from wm.seg.mgz... 112 voxels added to wm to prevent paths from MTL structures to cortex 1665 additional wm voxels added 0 additional wm voxels added SEG EDIT: 54557 voxels turned on, 59128 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 0 new 0 115,126,128 old 0 new 0 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 24 found - 24 modified | TOTAL: 24 pass 2 (xy+): 0 found - 24 modified | TOTAL: 24 pass 1 (xy-): 17 found - 17 modified | TOTAL: 41 pass 2 (xy-): 0 found - 17 modified | TOTAL: 41 pass 1 (yz+): 39 found - 39 modified | TOTAL: 80 pass 2 (yz+): 0 found - 39 modified | TOTAL: 80 pass 1 (yz-): 25 found - 25 modified | TOTAL: 105 pass 2 (yz-): 0 found - 25 modified | TOTAL: 105 pass 1 (xz+): 27 found - 27 modified | TOTAL: 132 pass 2 (xz+): 0 found - 27 modified | TOTAL: 132 pass 1 (xz-): 33 found - 33 modified | TOTAL: 165 pass 2 (xz-): 0 found - 33 modified | TOTAL: 165 Iteration Number : 1 pass 1 (+++): 18 found - 18 modified | TOTAL: 18 pass 2 (+++): 0 found - 18 modified | TOTAL: 18 pass 1 (+++): 22 found - 22 modified | TOTAL: 40 pass 2 (+++): 0 found - 22 modified | TOTAL: 40 pass 1 (+++): 27 found - 27 modified | TOTAL: 67 pass 2 (+++): 0 found - 27 modified | TOTAL: 67 pass 1 (+++): 21 found - 21 modified | TOTAL: 88 pass 2 (+++): 0 found - 21 modified | TOTAL: 88 Iteration Number : 1 pass 1 (++): 240 found - 240 modified | TOTAL: 240 pass 2 (++): 0 found - 240 modified | TOTAL: 240 pass 1 (+-): 212 found - 212 modified | TOTAL: 452 pass 2 (+-): 0 found - 212 modified | TOTAL: 452 pass 1 (--): 208 found - 208 modified | TOTAL: 660 pass 2 (--): 1 found - 209 modified | TOTAL: 661 pass 3 (--): 0 found - 209 modified | TOTAL: 661 pass 1 (-+): 227 found - 227 modified | TOTAL: 888 pass 2 (-+): 0 found - 227 modified | TOTAL: 888 Iteration Number : 2 pass 1 (xy+): 16 found - 16 modified | TOTAL: 16 pass 2 (xy+): 0 found - 16 modified | TOTAL: 16 pass 1 (xy-): 9 found - 9 modified | TOTAL: 25 pass 2 (xy-): 0 found - 9 modified | TOTAL: 25 pass 1 (yz+): 15 found - 15 modified | TOTAL: 40 pass 2 (yz+): 0 found - 15 modified | TOTAL: 40 pass 1 (yz-): 14 found - 14 modified | TOTAL: 54 pass 2 (yz-): 0 found - 14 modified | TOTAL: 54 pass 1 (xz+): 14 found - 14 modified | TOTAL: 68 pass 2 (xz+): 0 found - 14 modified | TOTAL: 68 pass 1 (xz-): 13 found - 13 modified | TOTAL: 81 pass 2 (xz-): 0 found - 13 modified | TOTAL: 81 Iteration Number : 2 pass 1 (+++): 1 found - 1 modified | TOTAL: 1 pass 2 (+++): 0 found - 1 modified | TOTAL: 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 1 pass 1 (+++): 1 found - 1 modified | TOTAL: 2 pass 2 (+++): 0 found - 1 modified | TOTAL: 2 pass 1 (+++): 2 found - 2 modified | TOTAL: 4 pass 2 (+++): 0 found - 2 modified | TOTAL: 4 Iteration Number : 2 pass 1 (++): 4 found - 4 modified | TOTAL: 4 pass 2 (++): 0 found - 4 modified | TOTAL: 4 pass 1 (+-): 7 found - 7 modified | TOTAL: 11 pass 2 (+-): 0 found - 7 modified | TOTAL: 11 pass 1 (--): 4 found - 4 modified | TOTAL: 15 pass 2 (--): 0 found - 4 modified | TOTAL: 15 pass 1 (-+): 10 found - 10 modified | TOTAL: 25 pass 2 (-+): 0 found - 10 modified | TOTAL: 25 Iteration Number : 3 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 1 found - 1 modified | TOTAL: 2 pass 2 (xy-): 0 found - 1 modified | TOTAL: 2 pass 1 (yz+): 1 found - 1 modified | TOTAL: 3 pass 2 (yz+): 0 found - 1 modified | TOTAL: 3 pass 1 (yz-): 1 found - 1 modified | TOTAL: 4 pass 2 (yz-): 0 found - 1 modified | TOTAL: 4 pass 1 (xz+): 2 found - 2 modified | TOTAL: 6 pass 2 (xz+): 0 found - 2 modified | TOTAL: 6 pass 1 (xz-): 0 found - 0 modified | TOTAL: 6 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 Iteration Number : 3 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 0 found - 0 modified | TOTAL: 1 pass 1 (--): 1 found - 1 modified | TOTAL: 2 pass 2 (--): 0 found - 1 modified | TOTAL: 2 pass 1 (-+): 0 found - 0 modified | TOTAL: 2 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 1 found - 1 modified | TOTAL: 1 pass 2 (yz+): 0 found - 1 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 5 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 5 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 5 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 1262 (out of 675958: 0.186698) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done mri_mask -transfer 255 -keep_mask_deletion_edits -xform /HD4/Subjects/s23_base/mri/transforms/subj_23_1_to_s23_base.lta wm.mgz /HD4/Subjects/subj_23_1/mri/wm.mgz wm.mgz transfer mask voxels=255 to dst vol Transferring mask edits ('1' voxels) to dst vol transform file name is /HD4/Subjects/s23_base/mri/transforms/subj_23_1_to_s23_base.lta DoAbs = 0 Apply the given LTA xfrom to the mask volume Reading transform ... Writing masked volume to wm.mgz...done. #-------------------------------------------- #@# Fill Mon Oct 16 23:49:25 EDT 2017 /HD4/Subjects/subj_23_1.long.s23_base/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.auto_noCCseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 0.993 -0.119 0.056 6.963; 0.080 1.071 0.350 -73.201; -0.090 -0.319 0.947 34.472; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 0.993 -0.119 0.056 6.963; 0.080 1.071 0.350 -73.201; -0.090 -0.319 0.947 34.472; 0.000 0.000 0.000 1.000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1745 (min = 350, max = 1400), aspect = 0.49 (min = 0.10, max = 0.75) need search nearby using seed (124, 118, 88), TAL = (4.0, -40.0, 10.0) talairach voxel to voxel transform 0.993 0.083 -0.089 2.265; -0.094 0.833 -0.302 72.074; 0.062 0.288 0.946 -11.939; 0.000 0.000 0.000 1.000; segmentation indicates cc at (124, 118, 88) --> (4.0, -40.0, 10.0) done. writing output to filled.mgz... filling took 0.6 minutes talairach cc position changed to (4.00, -40.00, 10.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(22.00, -40.00, 10.00) SRC: (109.45, 133.76, 111.96) search lh wm seed point around talairach space (-14.00, -40.00, 10.00), SRC: (145.18, 130.36, 114.21) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram to separate WM into two hemispheres ... Find the largest connected component for each hemisphere ... #-------------------------------------------- #@# Make White Surf lh Mon Oct 16 23:49:58 EDT 2017 cp -vf /HD4/Subjects/s23_base/surf/lh.white /HD4/Subjects/subj_23_1.long.s23_base/surf/lh.orig '/HD4/Subjects/s23_base/surf/lh.white' -> '/HD4/Subjects/subj_23_1.long.s23_base/surf/lh.orig' cp -vf /HD4/Subjects/s23_base/surf/lh.white /HD4/Subjects/subj_23_1.long.s23_base/surf/lh.orig_white '/HD4/Subjects/s23_base/surf/lh.white' -> '/HD4/Subjects/subj_23_1.long.s23_base/surf/lh.orig_white' cp -vf /HD4/Subjects/s23_base/surf/lh.pial /HD4/Subjects/subj_23_1.long.s23_base/surf/lh.orig_pial '/HD4/Subjects/s23_base/surf/lh.pial' -> '/HD4/Subjects/subj_23_1.long.s23_base/surf/lh.orig_pial' /HD4/Subjects/subj_23_1.long.s23_base/scripts mris_make_surfaces -orig_white orig_white -orig orig_white -long -max 3.5 -noaparc -whiteonly -mgz -T1 brain.finalsurfs subj_23_1.long.s23_base lh reading original vertex positions from orig_white only generating white matter surface using orig_white starting white location... Using longitudinal scheme using max_thickness = 3.5 not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /HD4/Subjects/subj_23_1.long.s23_base/mri/filled.mgz... reading volume /HD4/Subjects/subj_23_1.long.s23_base/mri/brain.finalsurfs.mgz... reading volume /HD4/Subjects/subj_23_1.long.s23_base/mri/wm.mgz... 27938 bright wm thresholded. 2566 bright non-wm voxels segmented. reading original surface position from /HD4/Subjects/subj_23_1.long.s23_base/surf/lh.orig_white... computing class statistics... border white: 310677 voxels (1.85%) border gray 334041 voxels (1.99%) WM (94.0): 95.0 +- 9.1 [70.0 --> 110.0] GM (79.0) : 77.6 +- 12.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 54.9 (was 70) setting MAX_BORDER_WHITE to 115.1 (was 105) setting MIN_BORDER_WHITE to 67.0 (was 85) setting MAX_CSF to 42.9 (was 40) setting MAX_GRAY to 96.9 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 61.0 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 30.8 (was 40) repositioning cortical surface to gray/white boundary reading volume /HD4/Subjects/subj_23_1.long.s23_base/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.90 +- 0.26 (0.04-->6.62) (max @ vno 67312 --> 145192) face area 0.34 +- 0.16 (0.00-->10.18) mean absolute distance = 0.64 +- 0.81 3221 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=106, GM=67 mean inside = 95.9, mean outside = 75.1 smoothing surface for 5 iterations... reading initial white vertex positions from orig_white... inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 1 vertex label from ripped group mean border=78.7, 86 (86) missing vertices, mean dist 0.4 [0.7 (%19.2)->0.6 (%80.8))] %67 local maxima, %28 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=local, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.94 +- 0.27 (0.08-->6.80) (max @ vno 63496 --> 63570) face area 0.34 +- 0.17 (0.00-->9.89) mean absolute distance = 0.35 +- 0.49 4092 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=6786569.0, rms=9.44 001: dt: 0.5000, sse=6232779.5, rms=6.091 (0.000%) 002: dt: 0.5000, sse=7274395.0, rms=4.620 (0.000%) 003: dt: 0.5000, sse=8018976.5, rms=4.152 (0.000%) 004: dt: 0.5000, sse=8310266.0, rms=3.907 (0.000%) rms = 3.89, time step reduction 1 of 3 to 0.250... 005: dt: 0.5000, sse=8464203.0, rms=3.889 (0.000%) 006: dt: 0.2500, sse=5746590.5, rms=2.737 (0.000%) 007: dt: 0.2500, sse=5496210.5, rms=2.368 (0.000%) 008: dt: 0.2500, sse=5243422.5, rms=2.310 (0.000%) 009: dt: 0.2500, sse=5228537.5, rms=2.239 (0.000%) rms = 2.23, time step reduction 2 of 3 to 0.125... 010: dt: 0.2500, sse=5152837.5, rms=2.228 (0.000%) 011: dt: 0.1250, sse=5031756.5, rms=2.140 (0.000%) rms = 2.13, time step reduction 3 of 3 to 0.062... 012: dt: 0.1250, sse=5003176.0, rms=2.132 (0.000%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group mean border=82.9, 84 (40) missing vertices, mean dist -0.2 [0.4 (%77.7)->0.2 (%22.3))] %85 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=local, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.92 +- 0.27 (0.05-->6.92) (max @ vno 63496 --> 63570) face area 0.37 +- 0.18 (0.00-->11.44) mean absolute distance = 0.22 +- 0.31 3323 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5795078.0, rms=5.55 013: dt: 0.5000, sse=6021920.0, rms=3.642 (0.000%) rms = 3.88, time step reduction 1 of 3 to 0.250... 014: dt: 0.2500, sse=5571038.5, rms=2.792 (0.000%) 015: dt: 0.2500, sse=5323611.5, rms=2.221 (0.000%) 016: dt: 0.2500, sse=5216425.5, rms=1.926 (0.000%) 017: dt: 0.2500, sse=5167451.0, rms=1.845 (0.000%) rms = 1.80, time step reduction 2 of 3 to 0.125... 018: dt: 0.2500, sse=5105317.0, rms=1.802 (0.000%) 019: dt: 0.1250, sse=5010861.5, rms=1.714 (0.000%) rms = 1.72, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=5010861.5, rms=1.714 (0.001%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group mean border=85.4, 57 (19) missing vertices, mean dist -0.1 [0.2 (%72.5)->0.2 (%27.5))] %92 local maxima, % 3 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=local, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.91 +- 0.26 (0.04-->7.01) (max @ vno 65969 --> 63570) face area 0.35 +- 0.18 (0.00-->11.14) mean absolute distance = 0.19 +- 0.27 3529 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5227493.0, rms=3.47 021: dt: 0.5000, sse=5621185.0, rms=3.343 (0.000%) rms = 3.73, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=5191095.5, rms=2.243 (0.000%) 023: dt: 0.2500, sse=5171086.5, rms=1.824 (0.000%) 024: dt: 0.2500, sse=5159867.0, rms=1.675 (0.000%) rms = 1.68, time step reduction 2 of 3 to 0.125... 025: dt: 0.1250, sse=5102692.0, rms=1.615 (0.000%) 026: dt: 0.1250, sse=5020872.0, rms=1.539 (0.000%) rms = 1.55, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=5020872.0, rms=1.539 (0.006%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group mean border=86.1, 33 (3) missing vertices, mean dist -0.0 [0.2 (%55.4)->0.2 (%44.6))] %93 local maxima, % 2 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=local, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /HD4/Subjects/subj_23_1.long.s23_base/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=5016554.5, rms=1.72 rms = 2.20, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=5166320.0, rms=1.286 (0.000%) 029: dt: 0.2500, sse=5421326.5, rms=1.143 (0.000%) rms = 1.15, time step reduction 2 of 3 to 0.125... rms = 1.14, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=5422362.0, rms=1.138 (0.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group generating cortex label... 14 non-cortical segments detected only using segment with 2205 vertices erasing segment 1 (vno[0] = 63609) erasing segment 2 (vno[0] = 73122) erasing segment 3 (vno[0] = 74944) erasing segment 4 (vno[0] = 87188) erasing segment 5 (vno[0] = 87218) erasing segment 6 (vno[0] = 101052) erasing segment 7 (vno[0] = 102142) erasing segment 8 (vno[0] = 106363) erasing segment 9 (vno[0] = 107340) erasing segment 10 (vno[0] = 108537) erasing segment 11 (vno[0] = 108547) erasing segment 12 (vno[0] = 110480) erasing segment 13 (vno[0] = 110668) writing cortex label to /HD4/Subjects/subj_23_1.long.s23_base/label/lh.cortex.label... writing curvature file /HD4/Subjects/subj_23_1.long.s23_base/surf/lh.curv writing smoothed area to lh.area writing curvature file /HD4/Subjects/subj_23_1.long.s23_base/surf/lh.area vertex spacing 0.91 +- 0.27 (0.06-->7.03) (max @ vno 65969 --> 63570) face area 0.35 +- 0.18 (0.00-->11.12) refinement took 4.2 minutes #-------------------------------------------- #@# Smooth2 lh Mon Oct 16 23:54:08 EDT 2017 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm /HD4/Subjects/subj_23_1.long.s23_base/scripts smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 lh Mon Oct 16 23:54:11 EDT 2017 /HD4/Subjects/subj_23_1.long.s23_base/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated avg radius = 48.9 mm, total surface area = 91819 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.116 (target=0.015) step 005: RMS=0.080 (target=0.015) step 010: RMS=0.057 (target=0.015) step 015: RMS=0.047 (target=0.015) step 020: RMS=0.038 (target=0.015) step 025: RMS=0.031 (target=0.015) step 030: RMS=0.026 (target=0.015) step 035: RMS=0.021 (target=0.015) step 040: RMS=0.018 (target=0.015) step 045: RMS=0.016 (target=0.015) inflation complete. inflation took 0.3 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 244 vertices thresholded to be in k1 ~ [-0.21 0.36], k2 ~ [-0.10 0.06] total integrated curvature = 0.591*4pi (7.433) --> 0 handles ICI = 1.9, FI = 12.2, variation=208.660 121 vertices thresholded to be in [-0.01 0.01] writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 146 vertices thresholded to be in [-0.12 0.19] done. writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.015, std = 0.025 done. #----------------------------------------- #@# Curvature Stats lh Mon Oct 16 23:55:37 EDT 2017 /HD4/Subjects/subj_23_1.long.s23_base/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm subj_23_1.long.s23_base lh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/lh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ subj_23_1.long.s23_base/lh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 249 ] Gb_filter = 0 WARN: S lookup min: -0.277955 WARN: S explicit min: 0.000000 vertex = 134 #-------------------------------------------- #@# Sphere lh Mon Oct 16 23:55:40 EDT 2017 /HD4/Subjects/subj_23_1.long.s23_base/scripts cp /HD4/Subjects/s23_base/surf/lh.sphere /HD4/Subjects/subj_23_1.long.s23_base/surf/lh.sphere #-------------------------------------------- #@# Surf Reg lh Mon Oct 16 23:55:40 EDT 2017 /HD4/Subjects/subj_23_1.long.s23_base/scripts mris_register -curv -nosulc -norot /HD4/Subjects/s23_base/surf/lh.sphere.reg /usr/local/freesurfer/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment disabling initial sulc alignment... disabling initial rigid alignment... $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading surface from /HD4/Subjects/s23_base/surf/lh.sphere.reg... reading template parameterization from /usr/local/freesurfer/average/lh.average.curvature.filled.buckner40.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=local, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 304 (130) use curv 16 no sulc 256 no rigid align 32 mris->nsize 1 mris->hemisphere 0 randomSeed 0 tol=5.0e-01, sigma=0.0, host=local, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization will not use the sulcal depth map will not rigidly align the surface tol=1.0e+00, sigma=0.0, host=local, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization -------------------- 2 Reading smoothwm curvature mean = -0.022, std = 0.270 curvature mean = 0.003, std = 0.065 curvature mean = 0.032, std = 0.401 curvature mean = 0.003, std = 0.079 curvature mean = 0.027, std = 0.573 curvature mean = 0.003, std = 0.086 curvature mean = 0.014, std = 0.719 curvature mean = 0.003, std = 0.089 curvature mean = 0.006, std = 0.826 MRISregister() return, current seed 0 writing registered surface to ../surf/lh.sphere.reg... #-------------------------------------------- #@# Jacobian white lh Tue Oct 17 00:00:49 EDT 2017 mris_jacobian ../surf/lh.white ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white... writing curvature file ../surf/lh.jacobian_white #-------------------------------------------- #@# AvgCurv lh Tue Oct 17 00:00:50 EDT 2017 /HD4/Subjects/subj_23_1.long.s23_base/scripts mrisp_paint -a 5 /usr/local/freesurfer/average/lh.average.curvature.filled.buckner40.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/lh.sphere.reg... reading template parameterization from /usr/local/freesurfer/average/lh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/lh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Tue Oct 17 00:00:52 EDT 2017 /HD4/Subjects/subj_23_1.long.s23_base/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 -long -R /HD4/Subjects/s23_base/label/lh.aparc.annot subj_23_1.long.s23_base lh ../surf/lh.sphere.reg /usr/local/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/lh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline will refine the initial labeling read-in from -R reading precomputed parcellation from /HD4/Subjects/s23_base/label/lh.aparc.annot... $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /usr/local/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs... reading color table from GCSA file.... average std = 1.0 using min determinant for regularization = 0.011 0 singular and 384 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) 000: 1273 changed, 145301 examined... 001: 296 changed, 6344 examined... 002: 82 changed, 1765 examined... 003: 22 changed, 508 examined... 004: 4 changed, 145 examined... 005: 1 changed, 28 examined... 006: 1 changed, 5 examined... 007: 0 changed, 5 examined... 000: 71 total segments, 20 labels (25 vertices) changed 001: 51 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 606 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 0 vertices marked for relabeling... 0 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 36 seconds. #-------------------------------------------- #@# Make Pial Surf lh Tue Oct 17 00:01:27 EDT 2017 /HD4/Subjects/subj_23_1.long.s23_base/scripts mris_make_surfaces -orig orig_white -orig_white orig_white -orig_pial orig_pial -long -max 3.5 -white NOWRITE -mgz -T1 brain.finalsurfs subj_23_1.long.s23_base lh reading original vertex positions from orig_white -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... using orig_white starting white location... using orig_pial starting pial locations... Using longitudinal scheme using max_thickness = 3.5 INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /HD4/Subjects/subj_23_1.long.s23_base/mri/filled.mgz... reading volume /HD4/Subjects/subj_23_1.long.s23_base/mri/brain.finalsurfs.mgz... reading volume /HD4/Subjects/subj_23_1.long.s23_base/mri/wm.mgz... 27938 bright wm thresholded. 2566 bright non-wm voxels segmented. reading original surface position from /HD4/Subjects/subj_23_1.long.s23_base/surf/lh.orig_white... computing class statistics... border white: 310677 voxels (1.85%) border gray 334041 voxels (1.99%) WM (94.0): 95.0 +- 9.1 [70.0 --> 110.0] GM (79.0) : 77.6 +- 12.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 54.9 (was 70) setting MAX_BORDER_WHITE to 115.1 (was 105) setting MIN_BORDER_WHITE to 67.0 (was 85) setting MAX_CSF to 42.9 (was 40) setting MAX_GRAY to 96.9 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 61.0 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 30.8 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=106, GM=67 mean inside = 95.9, mean outside = 75.1 smoothing surface for 5 iterations... reading initial white vertex positions from orig_white... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /HD4/Subjects/subj_23_1.long.s23_base/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.90 +- 0.26 (0.04-->6.62) (max @ vno 67312 --> 145192) face area 0.34 +- 0.16 (0.00-->10.18) mean absolute distance = 0.64 +- 0.81 3270 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 25 points - only 0.00% unknown deleting segment 2 with 369 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 3 with 4 points - only 0.00% unknown deleting segment 5 with 5 points - only 0.00% unknown deleting segment 7 with 11 points - only 0.00% unknown removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 1 vertex label from ripped group deleting segment 11 with 16 points - only 0.00% unknown deleting segment 12 with 5 points - only 0.00% unknown deleting segment 13 with 6 points - only 0.00% unknown mean border=78.7, 86 (86) missing vertices, mean dist 0.4 [0.7 (%19.2)->0.6 (%80.8))] %67 local maxima, %28 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=local, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.94 +- 0.27 (0.08-->6.80) (max @ vno 63496 --> 63570) face area 0.34 +- 0.17 (0.00-->9.89) mean absolute distance = 0.35 +- 0.50 4137 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=6801337.0, rms=9.44 001: dt: 0.5000, sse=6254410.5, rms=6.089 (0.000%) 002: dt: 0.5000, sse=7301973.5, rms=4.621 (0.000%) 003: dt: 0.5000, sse=8045010.5, rms=4.154 (0.000%) 004: dt: 0.5000, sse=8338012.0, rms=3.910 (0.000%) rms = 3.89, time step reduction 1 of 3 to 0.250... 005: dt: 0.5000, sse=8491542.0, rms=3.891 (0.000%) 006: dt: 0.2500, sse=5766917.0, rms=2.742 (0.000%) 007: dt: 0.2500, sse=5517619.0, rms=2.375 (0.000%) 008: dt: 0.2500, sse=5263621.0, rms=2.316 (0.000%) 009: dt: 0.2500, sse=5249315.5, rms=2.245 (0.000%) rms = 2.23, time step reduction 2 of 3 to 0.125... 010: dt: 0.2500, sse=5174176.0, rms=2.234 (0.000%) 011: dt: 0.1250, sse=5052569.0, rms=2.145 (0.000%) rms = 2.14, time step reduction 3 of 3 to 0.062... 012: dt: 0.1250, sse=5024246.5, rms=2.138 (0.000%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 5 points - only 0.00% unknown deleting segment 2 with 315 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 3 with 2 points - only 0.00% unknown deleting segment 4 with 26 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 7 with 22 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 8 with 4 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 9 with 2 points - only 0.00% unknown mean border=82.9, 84 (40) missing vertices, mean dist -0.2 [0.4 (%77.7)->0.2 (%22.3))] %86 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=local, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.92 +- 0.26 (0.05-->6.92) (max @ vno 63496 --> 63570) face area 0.37 +- 0.18 (0.00-->11.44) mean absolute distance = 0.23 +- 0.32 3368 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5818253.5, rms=5.55 013: dt: 0.5000, sse=6042523.0, rms=3.641 (0.000%) rms = 3.88, time step reduction 1 of 3 to 0.250... 014: dt: 0.2500, sse=5592613.0, rms=2.793 (0.000%) 015: dt: 0.2500, sse=5344844.0, rms=2.225 (0.000%) 016: dt: 0.2500, sse=5237617.5, rms=1.931 (0.000%) 017: dt: 0.2500, sse=5187846.5, rms=1.849 (0.000%) rms = 1.81, time step reduction 2 of 3 to 0.125... 018: dt: 0.2500, sse=5127190.5, rms=1.807 (0.000%) 019: dt: 0.1250, sse=5030936.0, rms=1.720 (0.000%) rms = 1.72, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=5030936.0, rms=1.720 (0.000%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 30 points - only 0.00% unknown deleting segment 2 with 325 points - only 0.00% unknown deleting segment 3 with 8 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 4 with 2 points - only 0.00% unknown deleting segment 5 with 27 points - only 0.00% unknown deleting segment 6 with 54 points - only 14.81% unknown removing 2 vertex label from ripped group deleting segment 8 with 24 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 9 with 4 points - only 0.00% unknown deleting segment 10 with 6 points - only 0.00% unknown mean border=85.4, 78 (31) missing vertices, mean dist -0.1 [0.2 (%72.4)->0.2 (%27.6))] %92 local maxima, % 3 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=local, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.92 +- 0.26 (0.04-->7.01) (max @ vno 65969 --> 63570) face area 0.35 +- 0.18 (0.00-->11.14) mean absolute distance = 0.19 +- 0.27 3564 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5250874.0, rms=3.47 021: dt: 0.5000, sse=5649631.0, rms=3.343 (0.000%) rms = 3.73, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=5217525.5, rms=2.245 (0.000%) 023: dt: 0.2500, sse=5200201.5, rms=1.827 (0.000%) 024: dt: 0.2500, sse=5188390.0, rms=1.679 (0.000%) rms = 1.69, time step reduction 2 of 3 to 0.125... 025: dt: 0.1250, sse=5131089.0, rms=1.619 (0.000%) 026: dt: 0.1250, sse=5049069.5, rms=1.543 (0.000%) rms = 1.55, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=5049069.5, rms=1.543 (0.007%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 6 points - only 0.00% unknown deleting segment 1 with 325 points - only 0.00% unknown deleting segment 2 with 17 points - only 0.00% unknown deleting segment 3 with 50 points - only 0.00% unknown deleting segment 5 with 83 points - only 7.23% unknown removing 2 vertex label from ripped group deleting segment 7 with 31 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 8 with 4 points - only 0.00% unknown deleting segment 9 with 6 points - only 0.00% unknown mean border=86.1, 78 (27) missing vertices, mean dist -0.0 [0.2 (%55.3)->0.2 (%44.7))] %93 local maxima, % 2 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=local, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=5052337.5, rms=1.72 rms = 2.20, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=5202857.0, rms=1.292 (0.000%) 029: dt: 0.2500, sse=5463120.5, rms=1.149 (0.000%) rms = 1.16, time step reduction 2 of 3 to 0.125... rms = 1.14, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=5464382.5, rms=1.144 (0.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group deleting segment 1 with 2 points - only 0.00% unknown smoothing surface for 5 iterations... reading initial pial vertex positions from orig_pial... mean border=56.2, 296 (296) missing vertices, mean dist 0.4 [0.3 (%22.7)->0.8 (%77.3))] %26 local maxima, %44 large gradients and %25 min vals, 1065 gradients ignored tol=1.0e-04, sigma=2.0, host=local, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=6822743.0, rms=10.77 001: dt: 0.5000, sse=6271303.0, rms=8.225 (0.000%) 002: dt: 0.5000, sse=6147303.0, rms=5.845 (0.000%) 003: dt: 0.5000, sse=6803792.0, rms=4.676 (0.000%) 004: dt: 0.5000, sse=7424526.5, rms=4.468 (0.000%) 005: dt: 0.5000, sse=7578009.5, rms=4.329 (0.000%) rms = 4.35, time step reduction 1 of 3 to 0.250... 006: dt: 0.2500, sse=6003041.5, rms=3.445 (0.000%) 007: dt: 0.2500, sse=5461140.0, rms=3.161 (0.000%) rms = 3.11, time step reduction 2 of 3 to 0.125... 008: dt: 0.2500, sse=5325328.5, rms=3.114 (0.000%) 009: dt: 0.1250, sse=5025879.0, rms=2.880 (0.000%) rms = 2.85, time step reduction 3 of 3 to 0.062... 010: dt: 0.1250, sse=4985443.0, rms=2.847 (0.000%) positioning took 0.9 minutes mean border=53.8, 1123 (98) missing vertices, mean dist 0.1 [0.2 (%42.8)->0.4 (%57.2))] %42 local maxima, %28 large gradients and %25 min vals, 643 gradients ignored tol=1.0e-04, sigma=1.0, host=local, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=5471479.0, rms=4.72 011: dt: 0.5000, sse=5890367.0, rms=4.286 (0.000%) rms = 4.42, time step reduction 1 of 3 to 0.250... 012: dt: 0.2500, sse=5416931.5, rms=3.392 (0.000%) 013: dt: 0.2500, sse=5557396.0, rms=3.115 (0.000%) 014: dt: 0.2500, sse=5508234.5, rms=3.050 (0.000%) rms = 3.05, time step reduction 2 of 3 to 0.125... 015: dt: 0.2500, sse=5604307.0, rms=3.048 (0.000%) 016: dt: 0.1250, sse=5294888.0, rms=2.764 (0.000%) rms = 2.72, time step reduction 3 of 3 to 0.062... 017: dt: 0.1250, sse=5287505.5, rms=2.716 (0.000%) positioning took 0.6 minutes mean border=51.9, 1349 (59) missing vertices, mean dist 0.1 [0.2 (%36.1)->0.3 (%63.9))] %55 local maxima, %15 large gradients and %25 min vals, 711 gradients ignored tol=1.0e-04, sigma=0.5, host=local, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=5482974.0, rms=3.74 rms = 4.43, time step reduction 1 of 3 to 0.250... 018: dt: 0.2500, sse=5266213.5, rms=3.141 (0.000%) 019: dt: 0.2500, sse=5339224.0, rms=2.932 (0.000%) rms = 2.91, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=5551600.0, rms=2.907 (0.000%) 021: dt: 0.1250, sse=5353237.0, rms=2.686 (0.000%) rms = 2.65, time step reduction 3 of 3 to 0.062... 022: dt: 0.1250, sse=5360125.0, rms=2.646 (0.000%) positioning took 0.5 minutes mean border=51.0, 2834 (55) missing vertices, mean dist 0.0 [0.2 (%45.0)->0.2 (%55.0))] %56 local maxima, %14 large gradients and %24 min vals, 579 gradients ignored tol=1.0e-04, sigma=0.2, host=local, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing pial surface to /HD4/Subjects/subj_23_1.long.s23_base/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=5393150.5, rms=2.88 rms = 3.81, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=5307314.0, rms=2.702 (0.000%) rms = 2.68, time step reduction 2 of 3 to 0.125... 024: dt: 0.2500, sse=5589016.0, rms=2.684 (0.000%) 025: dt: 0.1250, sse=5442467.5, rms=2.596 (0.000%) rms = 2.57, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=5487609.5, rms=2.567 (0.000%) positioning took 0.4 minutes writing curvature file /HD4/Subjects/subj_23_1.long.s23_base/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /HD4/Subjects/subj_23_1.long.s23_base/surf/lh.area.pial vertex spacing 1.02 +- 0.42 (0.09-->7.97) (max @ vno 65969 --> 63570) face area 0.41 +- 0.31 (0.00-->11.24) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 145301 vertices processed 25000 of 145301 vertices processed 50000 of 145301 vertices processed 75000 of 145301 vertices processed 100000 of 145301 vertices processed 125000 of 145301 vertices processed 0 of 145301 vertices processed 25000 of 145301 vertices processed 50000 of 145301 vertices processed 75000 of 145301 vertices processed 100000 of 145301 vertices processed 125000 of 145301 vertices processed thickness calculation complete, 617:817 truncations. 29617 vertices at 0 distance 101588 vertices at 1 distance 92620 vertices at 2 distance 36932 vertices at 3 distance 11481 vertices at 4 distance 3491 vertices at 5 distance 1036 vertices at 6 distance 340 vertices at 7 distance 144 vertices at 8 distance 77 vertices at 9 distance 53 vertices at 10 distance 48 vertices at 11 distance 21 vertices at 12 distance 17 vertices at 13 distance 17 vertices at 14 distance 17 vertices at 15 distance 14 vertices at 16 distance 15 vertices at 17 distance 14 vertices at 18 distance 6 vertices at 19 distance 4 vertices at 20 distance writing curvature file /HD4/Subjects/subj_23_1.long.s23_base/surf/lh.thickness positioning took 7.1 minutes #-------------------------------------------- #@# Surf Volume lh Tue Oct 17 00:08:31 EDT 2017 /HD4/Subjects/subj_23_1.long.s23_base/surf mris_calc -o lh.area.mid lh.area add lh.area.pial Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.area.mid lh.area.mid div 2 Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.volume lh.area.mid mul lh.thickness Saving result to 'lh.volume' (type = MRI_CURV_FILE) [ ok ] #----------------------------------------- #@# WM/GM Contrast lh Tue Oct 17 00:08:32 EDT 2017 /HD4/Subjects/subj_23_1.long.s23_base/scripts pctsurfcon --s subj_23_1.long.s23_base --lh-only Log file is /HD4/Subjects/subj_23_1.long.s23_base/scripts/pctsurfcon.log Tue Oct 17 00:08:32 EDT 2017 setenv SUBJECTS_DIR /HD4/Subjects cd /HD4/Subjects/subj_23_1.long.s23_base/scripts /usr/local/freesurfer/bin/pctsurfcon $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $ Linux localhost.localdomain 3.10.0-327.3.1.el7.x86_64 #1 SMP Wed Dec 9 14:09:15 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_vol2surf --mov /HD4/Subjects/subj_23_1.long.s23_base/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /HD4/Subjects/subj_23_1.long.s23_base/surf/tmp.pctsurfcon.9376/lh.wm.mgh --regheader subj_23_1.long.s23_base --cortex srcvol = /HD4/Subjects/subj_23_1.long.s23_base/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /HD4/Subjects/subj_23_1.long.s23_base/mri/orig.mgz as target reference. Loading label /HD4/Subjects/subj_23_1.long.s23_base/label/lh.cortex.label Reading surface /HD4/Subjects/subj_23_1.long.s23_base/surf/lh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 -1 -1 -1 using old Done mapping volume to surface Number of source voxels hit = 81987 Masking with /HD4/Subjects/subj_23_1.long.s23_base/label/lh.cortex.label Writing to /HD4/Subjects/subj_23_1.long.s23_base/surf/tmp.pctsurfcon.9376/lh.wm.mgh Dim: 145301 1 1 mri_vol2surf --mov /HD4/Subjects/subj_23_1.long.s23_base/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /HD4/Subjects/subj_23_1.long.s23_base/surf/tmp.pctsurfcon.9376/lh.gm.mgh --projfrac 0.3 --regheader subj_23_1.long.s23_base --cortex srcvol = /HD4/Subjects/subj_23_1.long.s23_base/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /HD4/Subjects/subj_23_1.long.s23_base/mri/orig.mgz as target reference. Loading label /HD4/Subjects/subj_23_1.long.s23_base/label/lh.cortex.label Reading surface /HD4/Subjects/subj_23_1.long.s23_base/surf/lh.white Done reading source surface Reading thickness /HD4/Subjects/subj_23_1.long.s23_base/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.3 0.3 0.3 using old Done mapping volume to surface Number of source voxels hit = 98224 Masking with /HD4/Subjects/subj_23_1.long.s23_base/label/lh.cortex.label Writing to /HD4/Subjects/subj_23_1.long.s23_base/surf/tmp.pctsurfcon.9376/lh.gm.mgh Dim: 145301 1 1 mri_concat /HD4/Subjects/subj_23_1.long.s23_base/surf/tmp.pctsurfcon.9376/lh.wm.mgh /HD4/Subjects/subj_23_1.long.s23_base/surf/tmp.pctsurfcon.9376/lh.gm.mgh --paired-diff-norm --mul 100 --o /HD4/Subjects/subj_23_1.long.s23_base/surf/lh.w-g.pct.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing Combining pairs nframes = 1 Multiplying by 100.000000 Writing to /HD4/Subjects/subj_23_1.long.s23_base/surf/lh.w-g.pct.mgh mri_segstats --in /HD4/Subjects/subj_23_1.long.s23_base/surf/lh.w-g.pct.mgh --annot subj_23_1.long.s23_base lh aparc --sum /HD4/Subjects/subj_23_1.long.s23_base/stats/lh.w-g.pct.stats --snr $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --in /HD4/Subjects/subj_23_1.long.s23_base/surf/lh.w-g.pct.mgh --annot subj_23_1.long.s23_base lh aparc --sum /HD4/Subjects/subj_23_1.long.s23_base/stats/lh.w-g.pct.stats --snr sysname Linux hostname localhost.localdomain machine x86_64 user mtobia UseRobust 0 Constructing seg from annotation Reading annotation reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Seg base 1000 Loading /HD4/Subjects/subj_23_1.long.s23_base/surf/lh.w-g.pct.mgh Vertex Area is 0.696281 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation 0 1000 unknown 0 0.000 1 1001 bankssts 2023 1465.755 2 1002 caudalanteriorcingulate 1033 736.327 3 1003 caudalmiddlefrontal 3317 2333.467 4 1004 corpuscallosum 0 0.000 5 1005 cuneus 2508 1710.054 6 1006 entorhinal 779 566.130 7 1007 fusiform 5113 3673.604 8 1008 inferiorparietal 7402 5283.255 9 1009 inferiortemporal 5584 4045.237 10 1010 isthmuscingulate 1885 1297.099 11 1011 lateraloccipital 8114 5567.687 12 1012 lateralorbitofrontal 3821 2750.852 13 1013 lingual 4968 3487.822 14 1014 medialorbitofrontal 2584 1824.958 15 1015 middletemporal 5178 3682.385 16 1016 parahippocampal 893 640.137 17 1017 paracentral 1902 1182.006 18 1018 parsopercularis 2711 1953.059 19 1019 parsorbitalis 924 662.430 20 1020 parstriangularis 2245 1561.859 21 1021 pericalcarine 2303 1634.718 22 1022 postcentral 6839 4509.098 23 1023 posteriorcingulate 1943 1339.242 24 1024 precentral 8251 5363.514 25 1025 precuneus 5685 3922.716 26 1026 rostralanteriorcingulate 1406 954.692 27 1027 rostralmiddlefrontal 8554 6160.122 28 1028 superiorfrontal 11677 8338.136 29 1029 superiorparietal 8117 5482.729 30 1030 superiortemporal 6345 4357.659 31 1031 supramarginal 6651 4680.049 32 1032 frontalpole 332 239.867 33 1033 temporalpole 741 547.688 34 1034 transversetemporal 793 493.146 35 1035 insula 3592 2450.243 Reporting on 34 segmentations mri_segstats done Cleaning up #----------------------------------------- #@# Parcellation Stats lh Tue Oct 17 00:08:37 EDT 2017 /HD4/Subjects/subj_23_1.long.s23_base/scripts mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab subj_23_1.long.s23_base lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /HD4/Subjects/subj_23_1.long.s23_base/mri/wm.mgz... reading input surface /HD4/Subjects/subj_23_1.long.s23_base/surf/lh.white... reading input pial surface /HD4/Subjects/subj_23_1.long.s23_base/surf/lh.pial... reading input white surface /HD4/Subjects/subj_23_1.long.s23_base/surf/lh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 2023 1466 3762 2.513 0.364 0.139 0.045 29 4.0 bankssts 1033 736 2305 2.819 0.910 0.183 0.058 26 2.6 caudalanteriorcingulate 3317 2333 6509 2.526 0.402 0.168 0.121 66 9.8 caudalmiddlefrontal 2508 1710 4238 2.239 0.482 0.180 0.072 57 7.1 cuneus 779 566 2769 3.476 0.870 0.152 0.053 10 1.8 entorhinal 5113 3674 11967 2.810 0.579 0.167 0.063 102 13.4 fusiform 7402 5283 14510 2.492 0.455 0.167 0.088 291 28.3 inferiorparietal 5584 4045 13816 2.876 0.613 0.166 0.069 118 15.2 inferiortemporal 1885 1297 3515 2.535 0.782 0.178 0.100 51 6.4 isthmuscingulate 8114 5568 14625 2.436 0.519 0.173 0.069 164 21.3 lateraloccipital 3821 2751 7932 2.615 0.616 0.177 0.085 111 12.1 lateralorbitofrontal 4968 3488 8129 2.183 0.649 0.183 0.084 102 18.1 lingual 2584 1825 4973 2.461 0.771 0.180 0.159 163 16.4 medialorbitofrontal 5178 3682 12721 2.895 0.549 0.173 0.077 158 15.5 middletemporal 893 640 2136 2.936 0.696 0.157 0.061 15 2.3 parahippocampal 1902 1182 3579 2.673 0.571 0.153 0.167 58 8.7 paracentral 2711 1953 5476 2.515 0.388 0.158 0.058 47 6.6 parsopercularis 924 662 1999 2.408 0.488 0.159 0.047 17 1.8 parsorbitalis 2245 1562 3869 2.299 0.445 0.147 0.047 37 4.5 parstriangularis 2303 1635 2689 1.824 0.514 0.169 0.064 35 6.2 pericalcarine 6839 4509 11612 2.288 0.548 0.154 0.066 128 21.2 postcentral 1943 1339 3282 2.245 0.772 0.175 0.091 53 6.8 posteriorcingulate 8251 5364 15534 2.690 0.518 0.156 0.075 155 26.4 precentral 5685 3923 10690 2.528 0.482 0.155 0.059 96 14.3 precuneus 1406 955 2974 2.786 0.768 0.179 0.081 36 4.9 rostralanteriorcingulate 8554 6160 16440 2.423 0.479 0.185 0.072 202 24.6 rostralmiddlefrontal 11677 8338 25438 2.671 0.498 0.165 0.064 209 33.1 superiorfrontal 8117 5483 13634 2.275 0.371 0.136 0.045 129 14.8 superiorparietal 6345 4358 15170 2.988 0.619 0.145 0.077 105 26.4 superiortemporal 6651 4680 13062 2.550 0.462 0.156 0.054 118 15.4 supramarginal 332 240 884 2.784 0.479 0.231 0.098 15 1.4 frontalpole 741 548 2876 4.037 0.539 0.193 0.090 18 2.9 temporalpole 793 493 1233 2.229 0.578 0.165 0.090 15 2.9 transversetemporal 3592 2450 7572 3.083 0.696 0.167 0.098 123 13.1 insula #----------------------------------------- #@# Cortical Parc 2 lh Tue Oct 17 00:08:50 EDT 2017 /HD4/Subjects/subj_23_1.long.s23_base/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 -long -R /HD4/Subjects/s23_base/label/lh.aparc.a2009s.annot subj_23_1.long.s23_base lh ../surf/lh.sphere.reg /usr/local/freesurfer/average/lh.destrieux.simple.2009-07-29.gcs ../label/lh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline will refine the initial labeling read-in from -R reading precomputed parcellation from /HD4/Subjects/s23_base/label/lh.aparc.a2009s.annot... $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /usr/local/freesurfer/average/lh.destrieux.simple.2009-07-29.gcs... reading color table from GCSA file.... average std = 3.9 0.2 using min determinant for regularization = 0.000 0 singular and 1066 ill-conditioned covariance matrices regularized input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) 000: 3069 changed, 145301 examined... 001: 804 changed, 14700 examined... 002: 200 changed, 4677 examined... 003: 81 changed, 1196 examined... 004: 30 changed, 484 examined... 005: 11 changed, 191 examined... 006: 5 changed, 69 examined... 007: 4 changed, 36 examined... 008: 2 changed, 32 examined... 009: 1 changed, 13 examined... 010: 0 changed, 7 examined... 000: 143 total segments, 51 labels (327 vertices) changed 001: 92 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 77 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 144 vertices marked for relabeling... 144 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 39 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Tue Oct 17 00:09:30 EDT 2017 /HD4/Subjects/subj_23_1.long.s23_base/scripts mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.a2009s.stats -b -a ../label/lh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab subj_23_1.long.s23_base lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /HD4/Subjects/subj_23_1.long.s23_base/mri/wm.mgz... reading input surface /HD4/Subjects/subj_23_1.long.s23_base/surf/lh.white... reading input pial surface /HD4/Subjects/subj_23_1.long.s23_base/surf/lh.pial... reading input white surface /HD4/Subjects/subj_23_1.long.s23_base/surf/lh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) Saving annotation colortable ../label/aparc.annot.a2009s.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1276 920 2377 2.407 0.540 0.178 0.066 32 3.1 G_and_S_frontomargin 1352 968 2689 2.444 0.648 0.163 0.055 23 3.0 G_and_S_occipital_inf 1414 804 2589 2.696 0.504 0.155 0.136 47 5.2 G_and_S_paracentral 1497 1065 3686 2.985 0.480 0.177 0.066 31 4.3 G_and_S_subcentral 812 611 2064 2.856 0.534 0.229 0.091 32 3.0 G_and_S_transv_frontopol 2220 1563 4484 2.626 0.517 0.152 0.057 40 5.3 G_and_S_cingul-Ant 1427 1048 3167 2.742 0.541 0.164 0.052 24 3.3 G_and_S_cingul-Mid-Ant 1331 967 2534 2.509 0.541 0.160 0.060 20 3.5 G_and_S_cingul-Mid-Post 703 485 1686 2.834 0.522 0.204 0.113 20 3.8 G_cingul-Post-dorsal 490 318 844 2.274 0.902 0.196 0.136 16 1.8 G_cingul-Post-ventral 2601 1767 4220 2.114 0.491 0.181 0.073 60 7.8 G_cuneus 1622 1138 3658 2.677 0.431 0.165 0.066 33 4.3 G_front_inf-Opercular 394 267 964 2.709 0.367 0.178 0.116 30 1.5 G_front_inf-Orbital 1271 871 2739 2.492 0.356 0.170 0.063 32 3.4 G_front_inf-Triangul 4663 3371 10744 2.581 0.453 0.203 0.127 139 17.4 G_front_middle 7997 5617 18911 2.773 0.503 0.176 0.088 179 28.6 G_front_sup 557 359 1338 3.151 0.670 0.141 0.090 10 1.7 G_Ins_lg_and_S_cent_ins 950 650 2801 3.539 0.840 0.241 0.197 78 6.3 G_insular_short 2264 1532 5241 2.745 0.438 0.195 0.160 207 17.0 G_occipital_middle 1595 1052 2764 2.323 0.394 0.141 0.047 27 3.0 G_occipital_sup 2115 1479 5326 2.851 0.543 0.188 0.076 54 7.1 G_oc-temp_lat-fusifor 3502 2417 5809 2.068 0.707 0.198 0.100 88 15.0 G_oc-temp_med-Lingual 1256 892 4128 3.337 0.820 0.164 0.069 29 3.6 G_oc-temp_med-Parahip 2470 1765 5912 2.649 0.642 0.190 0.089 74 8.4 G_orbital 2606 1863 5885 2.547 0.459 0.186 0.080 68 8.3 G_pariet_inf-Angular 3520 2466 8200 2.724 0.435 0.166 0.056 77 8.6 G_pariet_inf-Supramar 3642 2489 7345 2.403 0.343 0.143 0.049 77 7.1 G_parietal_sup 2613 1579 4782 2.361 0.440 0.159 0.087 70 11.2 G_postcentral 3152 1879 7075 2.897 0.446 0.156 0.081 71 9.8 G_precentral 2730 1868 6587 2.733 0.526 0.177 0.080 70 9.2 G_precuneus 878 655 2191 2.584 0.634 0.222 0.129 39 4.8 G_rectus 466 286 764 2.388 1.132 0.219 0.543 107 10.1 G_subcallosal 609 367 1065 2.313 0.557 0.177 0.337 21 14.0 G_temp_sup-G_T_transv 2417 1661 7491 3.178 0.624 0.172 0.071 57 7.5 G_temp_sup-Lateral 989 712 2794 3.578 0.627 0.134 0.054 16 2.5 G_temp_sup-Plan_polar 1340 949 2793 2.713 0.412 0.145 0.045 19 2.6 G_temp_sup-Plan_tempo 3116 2324 9219 3.015 0.615 0.185 0.084 82 10.3 G_temporal_inf 3181 2287 9183 3.037 0.552 0.186 0.090 127 10.6 G_temporal_middle 401 276 472 2.045 0.381 0.115 0.028 2 0.5 Lat_Fis-ant-Horizont 376 285 646 2.249 0.430 0.156 0.050 4 0.9 Lat_Fis-ant-Vertical 1261 890 1747 2.436 0.480 0.150 0.054 14 2.9 Lat_Fis-post 2547 1710 4268 2.277 0.596 0.188 0.081 62 8.1 Pole_occipital 2069 1515 7023 3.463 0.712 0.188 0.083 60 7.2 Pole_temporal 3170 2271 4210 2.076 0.548 0.158 0.057 41 7.7 S_calcarine 3647 2551 4744 2.109 0.528 0.160 0.075 56 13.0 S_central 901 633 1304 2.241 0.364 0.123 0.037 8 1.4 S_cingul-Marginalis 429 298 710 2.828 0.394 0.135 0.046 4 0.9 S_circular_insula_ant 1261 857 1975 2.877 0.495 0.099 0.026 6 1.4 S_circular_insula_inf 1934 1343 3034 2.633 0.435 0.128 0.041 15 3.4 S_circular_insula_sup 1362 992 2563 2.666 0.512 0.133 0.037 14 2.1 S_collat_transv_ant 256 197 531 2.403 0.367 0.153 0.049 3 0.6 S_collat_transv_post 2441 1734 3879 2.271 0.397 0.160 0.052 41 5.4 S_front_inf 1517 1087 2430 2.354 0.355 0.159 0.051 20 3.1 S_front_middle 3260 2324 5870 2.416 0.417 0.151 0.054 43 7.7 S_front_sup 591 389 832 2.429 0.511 0.129 0.037 5 0.9 S_interm_prim-Jensen 3093 2125 4292 2.192 0.362 0.136 0.046 34 5.7 S_intrapariet_and_P_trans 1572 1111 2373 2.309 0.327 0.153 0.048 20 3.0 S_oc_middle_and_Lunatus 1371 933 2094 2.340 0.383 0.133 0.055 15 2.2 S_oc_sup_and_transversal 718 521 1110 2.542 0.326 0.149 0.038 8 1.3 S_occipital_ant 1016 694 1425 2.485 0.293 0.137 0.044 9 1.8 S_oc-temp_lat 1948 1403 3318 2.608 0.441 0.145 0.051 22 3.9 S_oc-temp_med_and_Lingual 449 313 592 2.125 0.510 0.164 0.055 7 1.1 S_orbital_lateral 747 564 1195 2.121 0.611 0.134 0.041 7 1.3 S_orbital_med-olfact 1347 1000 2548 2.483 0.580 0.171 0.067 25 3.6 S_orbital-H_Shaped 2049 1424 3250 2.507 0.383 0.144 0.046 24 3.8 S_parieto_occipital 1610 972 1714 2.146 1.142 0.162 0.088 53 4.5 S_pericallosal 2967 2034 4016 2.214 0.367 0.140 0.049 36 6.4 S_postcentral 1431 997 2336 2.571 0.388 0.136 0.042 14 2.4 S_precentral-inf-part 1513 1075 2249 2.320 0.412 0.139 0.045 13 3.1 S_precentral-sup-part 655 466 1204 2.729 0.700 0.164 0.065 14 1.7 S_suborbital 939 670 1465 2.420 0.420 0.142 0.051 11 1.6 S_subparietal 1714 1163 2819 2.596 0.475 0.143 0.052 24 3.7 S_temporal_inf 6306 4552 11283 2.548 0.434 0.145 0.050 93 13.1 S_temporal_sup 307 213 352 1.883 0.426 0.160 0.065 4 0.9 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 lh Tue Oct 17 00:09:43 EDT 2017 /HD4/Subjects/subj_23_1.long.s23_base/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 -long -R /HD4/Subjects/s23_base/label/lh.aparc.DKTatlas40.annot subj_23_1.long.s23_base lh ../surf/lh.sphere.reg /usr/local/freesurfer/average/lh.DKTatlas40.gcs ../label/lh.aparc.DKTatlas40.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline will refine the initial labeling read-in from -R reading precomputed parcellation from /HD4/Subjects/s23_base/label/lh.aparc.DKTatlas40.annot... $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /usr/local/freesurfer/average/lh.DKTatlas40.gcs... reading color table from GCSA file.... average std = 0.9 using min determinant for regularization = 0.007 0 singular and 293 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature reading colortable from annotation file... colortable with 36 entries read (originally /Applications/freesurfer/average/colortable_desikan_killiany.txt) 000: 1320 changed, 145301 examined... 001: 334 changed, 6570 examined... 002: 119 changed, 2035 examined... 003: 60 changed, 729 examined... 004: 31 changed, 344 examined... 005: 15 changed, 183 examined... 006: 15 changed, 91 examined... 007: 12 changed, 89 examined... 008: 6 changed, 66 examined... 009: 2 changed, 32 examined... 010: 2 changed, 14 examined... 011: 1 changed, 14 examined... 012: 2 changed, 8 examined... 013: 1 changed, 9 examined... 014: 2 changed, 7 examined... 015: 2 changed, 14 examined... 016: 2 changed, 12 examined... 017: 2 changed, 12 examined... 018: 1 changed, 12 examined... 019: 0 changed, 7 examined... 000: 47 total segments, 14 labels (30 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 604 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 0 vertices marked for relabeling... 0 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas40.annot... classification took 0 minutes and 36 seconds. #----------------------------------------- #@# Parcellation Stats 3 lh Tue Oct 17 00:10:20 EDT 2017 /HD4/Subjects/subj_23_1.long.s23_base/scripts mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas40.stats -b -a ../label/lh.aparc.DKTatlas40.annot -c ../label/aparc.annot.DKTatlas40.ctab subj_23_1.long.s23_base lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot. reading volume /HD4/Subjects/subj_23_1.long.s23_base/mri/wm.mgz... reading input surface /HD4/Subjects/subj_23_1.long.s23_base/surf/lh.white... reading input pial surface /HD4/Subjects/subj_23_1.long.s23_base/surf/lh.pial... reading input white surface /HD4/Subjects/subj_23_1.long.s23_base/surf/lh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 36 entries read (originally /Applications/freesurfer/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.DKTatlas40.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1582 1129 3289 2.785 0.778 0.166 0.052 33 3.4 caudalanteriorcingulate 3388 2375 6630 2.525 0.404 0.169 0.121 68 10.1 caudalmiddlefrontal 3404 2331 5533 2.248 0.444 0.169 0.063 67 8.6 cuneus 728 527 2562 3.462 0.870 0.148 0.050 8 1.6 entorhinal 4558 3266 10149 2.755 0.541 0.164 0.061 82 11.6 fusiform 6885 4892 13531 2.502 0.464 0.168 0.091 282 27.2 inferiorparietal 5911 4290 14953 2.905 0.632 0.166 0.067 124 16.1 inferiortemporal 1985 1353 3595 2.502 0.813 0.175 0.097 52 6.5 isthmuscingulate 8422 5762 15204 2.426 0.518 0.171 0.068 168 21.7 lateraloccipital 4109 2978 8594 2.604 0.648 0.189 0.095 131 14.7 lateralorbitofrontal 4940 3466 8089 2.183 0.650 0.183 0.084 102 18.0 lingual 2274 1637 4574 2.488 0.671 0.177 0.084 64 7.9 medialorbitofrontal 6838 4920 16130 2.820 0.547 0.169 0.072 192 19.2 middletemporal 887 643 2153 2.955 0.707 0.159 0.061 15 2.3 parahippocampal 2208 1406 4183 2.668 0.555 0.151 0.151 61 9.4 paracentral 2388 1716 4747 2.541 0.362 0.159 0.059 41 6.1 parsopercularis 1182 812 2320 2.487 0.455 0.143 0.060 37 2.6 parsorbitalis 2686 1865 4732 2.290 0.462 0.152 0.050 49 5.6 parstriangularis 2273 1615 2660 1.827 0.515 0.168 0.064 35 6.1 pericalcarine 7494 4968 12713 2.296 0.546 0.153 0.064 136 22.7 postcentral 1976 1370 3392 2.300 0.749 0.178 0.092 54 7.0 posteriorcingulate 8260 5373 15550 2.696 0.512 0.156 0.074 155 26.3 precentral 5513 3814 10687 2.527 0.482 0.154 0.059 94 13.8 precuneus 1809 1203 3551 2.659 0.881 0.185 0.191 138 14.0 rostralanteriorcingulate 5946 4264 11330 2.409 0.484 0.182 0.070 132 16.6 rostralmiddlefrontal 13091 9397 28659 2.645 0.504 0.172 0.068 264 38.5 superiorfrontal 6426 4318 10733 2.277 0.369 0.136 0.047 108 11.9 superiorparietal 8623 6023 20947 3.006 0.676 0.149 0.073 148 32.7 superiortemporal 6617 4615 12854 2.546 0.463 0.157 0.055 120 15.5 supramarginal 809 499 1238 2.198 0.578 0.166 0.090 15 3.0 transversetemporal 3001 2072 6638 3.112 0.701 0.157 0.084 84 9.3 insula #-------------------------------------------- #@# Make White Surf rh Tue Oct 17 00:10:33 EDT 2017 cp -vf /HD4/Subjects/s23_base/surf/rh.white /HD4/Subjects/subj_23_1.long.s23_base/surf/rh.orig '/HD4/Subjects/s23_base/surf/rh.white' -> '/HD4/Subjects/subj_23_1.long.s23_base/surf/rh.orig' cp -vf /HD4/Subjects/s23_base/surf/rh.white /HD4/Subjects/subj_23_1.long.s23_base/surf/rh.orig_white '/HD4/Subjects/s23_base/surf/rh.white' -> '/HD4/Subjects/subj_23_1.long.s23_base/surf/rh.orig_white' cp -vf /HD4/Subjects/s23_base/surf/rh.pial /HD4/Subjects/subj_23_1.long.s23_base/surf/rh.orig_pial '/HD4/Subjects/s23_base/surf/rh.pial' -> '/HD4/Subjects/subj_23_1.long.s23_base/surf/rh.orig_pial' /HD4/Subjects/subj_23_1.long.s23_base/scripts mris_make_surfaces -orig_white orig_white -orig orig_white -long -max 3.5 -noaparc -whiteonly -mgz -T1 brain.finalsurfs subj_23_1.long.s23_base rh reading original vertex positions from orig_white only generating white matter surface using orig_white starting white location... Using longitudinal scheme using max_thickness = 3.5 not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /HD4/Subjects/subj_23_1.long.s23_base/mri/filled.mgz... reading volume /HD4/Subjects/subj_23_1.long.s23_base/mri/brain.finalsurfs.mgz... reading volume /HD4/Subjects/subj_23_1.long.s23_base/mri/wm.mgz... 26626 bright wm thresholded. 2562 bright non-wm voxels segmented. reading original surface position from /HD4/Subjects/subj_23_1.long.s23_base/surf/rh.orig_white... computing class statistics... border white: 310677 voxels (1.85%) border gray 334041 voxels (1.99%) WM (94.0): 95.0 +- 9.0 [70.0 --> 110.0] GM (80.0) : 77.6 +- 12.3 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 55.7 (was 70) setting MAX_BORDER_WHITE to 115.0 (was 105) setting MIN_BORDER_WHITE to 68.0 (was 85) setting MAX_CSF to 43.5 (was 40) setting MAX_GRAY to 97.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 61.9 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 31.2 (was 40) repositioning cortical surface to gray/white boundary reading volume /HD4/Subjects/subj_23_1.long.s23_base/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.89 +- 0.25 (0.02-->3.50) (max @ vno 95756 --> 96889) face area 0.33 +- 0.15 (0.00-->2.03) mean absolute distance = 0.62 +- 0.81 3712 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=106, GM=68 mean inside = 96.0, mean outside = 75.3 smoothing surface for 5 iterations... reading initial white vertex positions from orig_white... inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 1 vertex label from ripped group removing 1 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group mean border=79.6, 57 (57) missing vertices, mean dist 0.4 [0.7 (%19.3)->0.6 (%80.7))] %64 local maxima, %31 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=local, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.93 +- 0.26 (0.10-->3.70) (max @ vno 118526 --> 118503) face area 0.33 +- 0.16 (0.00-->2.25) mean absolute distance = 0.34 +- 0.51 3713 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=6560884.5, rms=8.98 001: dt: 0.5000, sse=6168198.5, rms=5.862 (0.000%) 002: dt: 0.5000, sse=7215040.0, rms=4.550 (0.000%) 003: dt: 0.5000, sse=7838623.0, rms=4.126 (0.000%) 004: dt: 0.5000, sse=8111133.0, rms=3.908 (0.000%) rms = 3.90, time step reduction 1 of 3 to 0.250... 005: dt: 0.5000, sse=8213606.5, rms=3.896 (0.000%) 006: dt: 0.2500, sse=5620663.0, rms=2.706 (0.000%) 007: dt: 0.2500, sse=5383201.0, rms=2.323 (0.000%) rms = 2.28, time step reduction 2 of 3 to 0.125... 008: dt: 0.2500, sse=5140805.0, rms=2.280 (0.000%) 009: dt: 0.1250, sse=4962060.0, rms=2.120 (0.000%) rms = 2.10, time step reduction 3 of 3 to 0.062... 010: dt: 0.1250, sse=4915345.0, rms=2.100 (0.000%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 2 vertex label from ripped group mean border=83.6, 29 (8) missing vertices, mean dist -0.2 [0.4 (%76.3)->0.2 (%23.7))] %82 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=local, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.92 +- 0.26 (0.04-->3.90) (max @ vno 95767 --> 95782) face area 0.36 +- 0.18 (0.00-->2.92) mean absolute distance = 0.23 +- 0.33 3587 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5653262.0, rms=5.35 011: dt: 0.5000, sse=5887758.5, rms=3.768 (0.000%) rms = 3.94, time step reduction 1 of 3 to 0.250... 012: dt: 0.2500, sse=5432559.0, rms=2.917 (0.000%) 013: dt: 0.2500, sse=5202807.5, rms=2.310 (0.000%) 014: dt: 0.2500, sse=5105280.5, rms=1.967 (0.000%) 015: dt: 0.2500, sse=5057491.0, rms=1.856 (0.000%) 016: dt: 0.2500, sse=5004411.0, rms=1.800 (0.000%) rms = 1.78, time step reduction 2 of 3 to 0.125... 017: dt: 0.2500, sse=4993794.0, rms=1.783 (0.000%) 018: dt: 0.1250, sse=4887550.5, rms=1.694 (0.000%) rms = 1.70, time step reduction 3 of 3 to 0.062... 019: dt: 0.1250, sse=4887550.5, rms=1.694 (0.001%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group mean border=86.0, 30 (4) missing vertices, mean dist -0.1 [0.2 (%71.7)->0.2 (%28.3))] %90 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=local, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.91 +- 0.26 (0.09-->4.13) (max @ vno 95767 --> 95782) face area 0.35 +- 0.17 (0.00-->3.04) mean absolute distance = 0.19 +- 0.28 3719 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5118146.0, rms=3.48 020: dt: 0.5000, sse=5516444.5, rms=3.333 (0.000%) rms = 3.72, time step reduction 1 of 3 to 0.250... 021: dt: 0.2500, sse=5093472.0, rms=2.246 (0.000%) 022: dt: 0.2500, sse=5066200.5, rms=1.808 (0.000%) 023: dt: 0.2500, sse=5054981.0, rms=1.669 (0.000%) rms = 1.68, time step reduction 2 of 3 to 0.125... 024: dt: 0.1250, sse=4997466.5, rms=1.603 (0.000%) 025: dt: 0.1250, sse=4916737.0, rms=1.517 (0.000%) rms = 1.52, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=4916737.0, rms=1.517 (0.002%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group mean border=86.7, 45 (3) missing vertices, mean dist -0.0 [0.2 (%55.0)->0.2 (%45.0))] %91 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=local, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /HD4/Subjects/subj_23_1.long.s23_base/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=4927909.5, rms=1.72 rms = 2.20, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=5064826.5, rms=1.287 (0.000%) 028: dt: 0.2500, sse=5322871.5, rms=1.131 (0.000%) rms = 1.14, time step reduction 2 of 3 to 0.125... rms = 1.12, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=5322566.5, rms=1.124 (0.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 1 vertex label from ripped group generating cortex label... 9 non-cortical segments detected only using segment with 2572 vertices erasing segment 1 (vno[0] = 66179) erasing segment 2 (vno[0] = 82213) erasing segment 3 (vno[0] = 94748) erasing segment 4 (vno[0] = 107459) erasing segment 5 (vno[0] = 110701) erasing segment 6 (vno[0] = 111788) erasing segment 7 (vno[0] = 118514) erasing segment 8 (vno[0] = 120201) writing cortex label to /HD4/Subjects/subj_23_1.long.s23_base/label/rh.cortex.label... writing curvature file /HD4/Subjects/subj_23_1.long.s23_base/surf/rh.curv writing smoothed area to rh.area writing curvature file /HD4/Subjects/subj_23_1.long.s23_base/surf/rh.area vertex spacing 0.91 +- 0.26 (0.05-->4.15) (max @ vno 95767 --> 95782) face area 0.35 +- 0.17 (0.00-->3.07) refinement took 4.1 minutes #-------------------------------------------- #@# Smooth2 rh Tue Oct 17 00:14:38 EDT 2017 mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm /HD4/Subjects/subj_23_1.long.s23_base/scripts smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 rh Tue Oct 17 00:14:41 EDT 2017 /HD4/Subjects/subj_23_1.long.s23_base/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated avg radius = 49.8 mm, total surface area = 92830 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.115 (target=0.015) step 005: RMS=0.079 (target=0.015) step 010: RMS=0.058 (target=0.015) step 015: RMS=0.047 (target=0.015) step 020: RMS=0.038 (target=0.015) step 025: RMS=0.032 (target=0.015) step 030: RMS=0.026 (target=0.015) step 035: RMS=0.022 (target=0.015) step 040: RMS=0.019 (target=0.015) step 045: RMS=0.017 (target=0.015) step 050: RMS=0.015 (target=0.015) inflation complete. inflation took 0.3 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/rh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 169 vertices thresholded to be in k1 ~ [-0.21 0.33], k2 ~ [-0.13 0.07] total integrated curvature = 0.618*4pi (7.763) --> 0 handles ICI = 1.8, FI = 11.1, variation=191.158 119 vertices thresholded to be in [-0.01 0.01] writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 136 vertices thresholded to be in [-0.12 0.15] done. writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.015, std = 0.024 done. #----------------------------------------- #@# Curvature Stats rh Tue Oct 17 00:16:04 EDT 2017 /HD4/Subjects/subj_23_1.long.s23_base/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm subj_23_1.long.s23_base rh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/rh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ subj_23_1.long.s23_base/rh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 251 ] Gb_filter = 0 WARN: S lookup min: -0.335677 WARN: S explicit min: 0.000000 vertex = 11 #-------------------------------------------- #@# Sphere rh Tue Oct 17 00:16:07 EDT 2017 /HD4/Subjects/subj_23_1.long.s23_base/scripts cp /HD4/Subjects/s23_base/surf/rh.sphere /HD4/Subjects/subj_23_1.long.s23_base/surf/rh.sphere #-------------------------------------------- #@# Surf Reg rh Tue Oct 17 00:16:07 EDT 2017 /HD4/Subjects/subj_23_1.long.s23_base/scripts mris_register -curv -nosulc -norot /HD4/Subjects/s23_base/surf/rh.sphere.reg /usr/local/freesurfer/average/rh.average.curvature.filled.buckner40.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment disabling initial sulc alignment... disabling initial rigid alignment... $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading surface from /HD4/Subjects/s23_base/surf/rh.sphere.reg... reading template parameterization from /usr/local/freesurfer/average/rh.average.curvature.filled.buckner40.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=local, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 304 (130) use curv 16 no sulc 256 no rigid align 32 mris->nsize 1 mris->hemisphere 1 randomSeed 0 tol=5.0e-01, sigma=0.0, host=local, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization will not use the sulcal depth map will not rigidly align the surface tol=1.0e+00, sigma=0.0, host=local, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization -------------------- 2 Reading smoothwm curvature mean = -0.021, std = 0.286 curvature mean = 0.006, std = 0.068 curvature mean = 0.029, std = 0.376 curvature mean = 0.005, std = 0.083 curvature mean = 0.023, std = 0.537 curvature mean = 0.005, std = 0.090 curvature mean = 0.013, std = 0.670 curvature mean = 0.006, std = 0.093 curvature mean = 0.005, std = 0.773 MRISregister() return, current seed 0 writing registered surface to ../surf/rh.sphere.reg... expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white rh Tue Oct 17 00:21:31 EDT 2017 mris_jacobian ../surf/rh.white ../surf/rh.sphere.reg ../surf/rh.jacobian_white reading surface from ../surf/rh.white... writing curvature file ../surf/rh.jacobian_white #-------------------------------------------- #@# AvgCurv rh Tue Oct 17 00:21:32 EDT 2017 /HD4/Subjects/subj_23_1.long.s23_base/scripts mrisp_paint -a 5 /usr/local/freesurfer/average/rh.average.curvature.filled.buckner40.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/rh.sphere.reg... reading template parameterization from /usr/local/freesurfer/average/rh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc rh Tue Oct 17 00:21:34 EDT 2017 /HD4/Subjects/subj_23_1.long.s23_base/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 -long -R /HD4/Subjects/s23_base/label/rh.aparc.annot subj_23_1.long.s23_base rh ../surf/rh.sphere.reg /usr/local/freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/rh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline will refine the initial labeling read-in from -R reading precomputed parcellation from /HD4/Subjects/s23_base/label/rh.aparc.annot... $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /usr/local/freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs... reading color table from GCSA file.... average std = 0.7 using min determinant for regularization = 0.006 0 singular and 311 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) 000: 1243 changed, 147659 examined... 001: 297 changed, 6159 examined... 002: 78 changed, 1781 examined... 003: 30 changed, 476 examined... 004: 10 changed, 196 examined... 005: 4 changed, 52 examined... 006: 3 changed, 25 examined... 007: 0 changed, 12 examined... 000: 75 total segments, 26 labels (36 vertices) changed 001: 49 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 735 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 0 vertices marked for relabeling... 0 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 36 seconds. #-------------------------------------------- #@# Make Pial Surf rh Tue Oct 17 00:22:10 EDT 2017 /HD4/Subjects/subj_23_1.long.s23_base/scripts mris_make_surfaces -orig orig_white -orig_white orig_white -orig_pial orig_pial -long -max 3.5 -white NOWRITE -mgz -T1 brain.finalsurfs subj_23_1.long.s23_base rh reading original vertex positions from orig_white -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... using orig_white starting white location... using orig_pial starting pial locations... Using longitudinal scheme using max_thickness = 3.5 INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /HD4/Subjects/subj_23_1.long.s23_base/mri/filled.mgz... reading volume /HD4/Subjects/subj_23_1.long.s23_base/mri/brain.finalsurfs.mgz... reading volume /HD4/Subjects/subj_23_1.long.s23_base/mri/wm.mgz... 26626 bright wm thresholded. 2562 bright non-wm voxels segmented. reading original surface position from /HD4/Subjects/subj_23_1.long.s23_base/surf/rh.orig_white... computing class statistics... border white: 310677 voxels (1.85%) border gray 334041 voxels (1.99%) WM (94.0): 95.0 +- 9.0 [70.0 --> 110.0] GM (80.0) : 77.6 +- 12.3 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 55.7 (was 70) setting MAX_BORDER_WHITE to 115.0 (was 105) setting MIN_BORDER_WHITE to 68.0 (was 85) setting MAX_CSF to 43.5 (was 40) setting MAX_GRAY to 97.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 61.9 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 31.2 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=106, GM=68 mean inside = 96.0, mean outside = 75.3 smoothing surface for 5 iterations... reading initial white vertex positions from orig_white... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /HD4/Subjects/subj_23_1.long.s23_base/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.89 +- 0.25 (0.02-->3.50) (max @ vno 95756 --> 96889) face area 0.33 +- 0.15 (0.00-->2.03) mean absolute distance = 0.62 +- 0.81 3736 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group deleting segment 1 with 2 points - only 0.00% unknown removing 1 vertex label from ripped group removing 1 vertex label from ripped group deleting segment 3 with 1 points - only 0.00% unknown deleting segment 4 with 225 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 7 with 11 points - only 0.00% unknown deleting segment 8 with 41 points - only 0.00% unknown removing 4 vertex label from ripped group mean border=79.6, 57 (57) missing vertices, mean dist 0.3 [0.7 (%19.3)->0.6 (%80.7))] %64 local maxima, %31 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=local, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.94 +- 0.26 (0.10-->3.70) (max @ vno 118526 --> 118503) face area 0.33 +- 0.16 (0.00-->2.18) mean absolute distance = 0.34 +- 0.51 3717 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=6569871.0, rms=8.97 001: dt: 0.5000, sse=6183993.0, rms=5.861 (0.000%) 002: dt: 0.5000, sse=7232836.5, rms=4.550 (0.000%) 003: dt: 0.5000, sse=7855963.0, rms=4.125 (0.000%) 004: dt: 0.5000, sse=8131995.0, rms=3.908 (0.000%) rms = 3.90, time step reduction 1 of 3 to 0.250... 005: dt: 0.5000, sse=8233260.0, rms=3.895 (0.000%) 006: dt: 0.2500, sse=5632779.0, rms=2.706 (0.000%) 007: dt: 0.2500, sse=5393180.0, rms=2.324 (0.000%) rms = 2.28, time step reduction 2 of 3 to 0.125... 008: dt: 0.2500, sse=5150588.5, rms=2.281 (0.000%) 009: dt: 0.1250, sse=4972021.5, rms=2.121 (0.000%) rms = 2.10, time step reduction 3 of 3 to 0.062... 010: dt: 0.1250, sse=4925413.5, rms=2.102 (0.000%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 5 with 192 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 6 with 4 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 8 with 38 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 9 with 3 points - only 0.00% unknown mean border=83.6, 29 (8) missing vertices, mean dist -0.2 [0.4 (%76.3)->0.2 (%23.7))] %83 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=local, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.92 +- 0.26 (0.04-->3.79) (max @ vno 118526 --> 118503) face area 0.36 +- 0.17 (0.00-->2.47) mean absolute distance = 0.23 +- 0.33 3598 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5663942.5, rms=5.35 011: dt: 0.5000, sse=5898565.5, rms=3.766 (0.000%) rms = 3.94, time step reduction 1 of 3 to 0.250... 012: dt: 0.2500, sse=5443145.0, rms=2.916 (0.000%) 013: dt: 0.2500, sse=5215350.0, rms=2.309 (0.000%) 014: dt: 0.2500, sse=5114704.5, rms=1.967 (0.000%) 015: dt: 0.2500, sse=5068056.5, rms=1.857 (0.000%) 016: dt: 0.2500, sse=5016159.0, rms=1.801 (0.000%) rms = 1.78, time step reduction 2 of 3 to 0.125... 017: dt: 0.2500, sse=5004315.0, rms=1.784 (0.000%) 018: dt: 0.1250, sse=4897883.0, rms=1.695 (0.000%) rms = 1.70, time step reduction 3 of 3 to 0.062... 019: dt: 0.1250, sse=4897883.0, rms=1.695 (0.001%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 2 vertex label from ripped group deleting segment 1 with 2 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 3 with 196 points - only 0.00% unknown deleting segment 4 with 7 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 6 with 48 points - only 0.00% unknown deleting segment 7 with 8 points - only 0.00% unknown mean border=86.0, 30 (4) missing vertices, mean dist -0.1 [0.2 (%71.7)->0.2 (%28.3))] %90 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=local, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.91 +- 0.26 (0.09-->3.80) (max @ vno 118526 --> 118503) face area 0.35 +- 0.17 (0.00-->2.38) mean absolute distance = 0.19 +- 0.28 3735 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5128967.0, rms=3.48 020: dt: 0.5000, sse=5528292.0, rms=3.333 (0.000%) rms = 3.72, time step reduction 1 of 3 to 0.250... 021: dt: 0.2500, sse=5104337.0, rms=2.247 (0.000%) 022: dt: 0.2500, sse=5078192.5, rms=1.809 (0.000%) 023: dt: 0.2500, sse=5066824.0, rms=1.670 (0.000%) rms = 1.68, time step reduction 2 of 3 to 0.125... 024: dt: 0.1250, sse=5009047.0, rms=1.604 (0.000%) 025: dt: 0.1250, sse=4927915.5, rms=1.518 (0.000%) rms = 1.52, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=4927915.5, rms=1.518 (0.002%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 2 vertex label from ripped group deleting segment 1 with 2 points - only 0.00% unknown deleting segment 2 with 216 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 4 with 48 points - only 0.00% unknown deleting segment 5 with 7 points - only 0.00% unknown mean border=86.7, 44 (3) missing vertices, mean dist -0.0 [0.2 (%55.0)->0.2 (%45.0))] %91 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=local, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=4939096.0, rms=1.72 rms = 2.20, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=5077358.5, rms=1.287 (0.000%) 028: dt: 0.2500, sse=5336577.0, rms=1.131 (0.000%) rms = 1.14, time step reduction 2 of 3 to 0.125... rms = 1.12, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=5336384.5, rms=1.125 (0.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 1 vertex label from ripped group smoothing surface for 5 iterations... reading initial pial vertex positions from orig_pial... mean border=56.6, 319 (319) missing vertices, mean dist 0.4 [0.3 (%24.3)->0.7 (%75.7))] %26 local maxima, %46 large gradients and %23 min vals, 1001 gradients ignored tol=1.0e-04, sigma=2.0, host=local, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=7039540.0, rms=10.91 001: dt: 0.5000, sse=6422522.5, rms=8.290 (0.000%) 002: dt: 0.5000, sse=6248469.5, rms=5.932 (0.000%) 003: dt: 0.5000, sse=6808437.0, rms=4.747 (0.000%) 004: dt: 0.5000, sse=7430139.0, rms=4.543 (0.000%) 005: dt: 0.5000, sse=7569640.0, rms=4.411 (0.000%) rms = 4.45, time step reduction 1 of 3 to 0.250... 006: dt: 0.2500, sse=6005692.5, rms=3.523 (0.000%) 007: dt: 0.2500, sse=5497649.5, rms=3.234 (0.000%) rms = 3.20, time step reduction 2 of 3 to 0.125... 008: dt: 0.2500, sse=5358950.5, rms=3.196 (0.000%) 009: dt: 0.1250, sse=5059819.5, rms=2.942 (0.000%) rms = 2.91, time step reduction 3 of 3 to 0.062... 010: dt: 0.1250, sse=5018671.5, rms=2.906 (0.000%) positioning took 0.9 minutes mean border=54.3, 1157 (105) missing vertices, mean dist 0.1 [0.2 (%43.1)->0.4 (%56.9))] %43 local maxima, %29 large gradients and %23 min vals, 507 gradients ignored tol=1.0e-04, sigma=1.0, host=local, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=5512654.0, rms=4.77 011: dt: 0.5000, sse=5941131.0, rms=4.412 (0.000%) rms = 4.55, time step reduction 1 of 3 to 0.250... 012: dt: 0.2500, sse=5452405.5, rms=3.533 (0.000%) 013: dt: 0.2500, sse=5559561.0, rms=3.257 (0.000%) 014: dt: 0.2500, sse=5507098.5, rms=3.178 (0.000%) rms = 3.16, time step reduction 2 of 3 to 0.125... 015: dt: 0.2500, sse=5594692.0, rms=3.165 (0.000%) 016: dt: 0.1250, sse=5281989.0, rms=2.856 (0.000%) 017: dt: 0.1250, sse=5270485.5, rms=2.804 (0.000%) rms = 2.80, time step reduction 3 of 3 to 0.062... 018: dt: 0.1250, sse=5259317.0, rms=2.801 (0.000%) positioning took 0.7 minutes mean border=52.2, 1432 (73) missing vertices, mean dist 0.1 [0.2 (%34.4)->0.3 (%65.6))] %57 local maxima, %15 large gradients and %23 min vals, 653 gradients ignored tol=1.0e-04, sigma=0.5, host=local, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=5494153.5, rms=3.97 rms = 4.47, time step reduction 1 of 3 to 0.250... 019: dt: 0.2500, sse=5271151.5, rms=3.351 (0.000%) 020: dt: 0.2500, sse=5298912.5, rms=3.071 (0.000%) 021: dt: 0.2500, sse=5513776.5, rms=3.008 (0.000%) rms = 3.04, time step reduction 2 of 3 to 0.125... 022: dt: 0.1250, sse=5425114.5, rms=2.904 (0.000%) 023: dt: 0.1250, sse=5354195.0, rms=2.755 (0.000%) rms = 2.72, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=5340645.0, rms=2.725 (0.000%) positioning took 0.6 minutes mean border=51.3, 2857 (61) missing vertices, mean dist 0.0 [0.2 (%44.0)->0.2 (%56.0))] %58 local maxima, %14 large gradients and %22 min vals, 538 gradients ignored tol=1.0e-04, sigma=0.2, host=local, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing pial surface to /HD4/Subjects/subj_23_1.long.s23_base/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=5381898.0, rms=3.01 rms = 3.93, time step reduction 1 of 3 to 0.250... 025: dt: 0.2500, sse=5287560.5, rms=2.809 (0.000%) rms = 2.76, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=5541771.0, rms=2.763 (0.000%) 027: dt: 0.1250, sse=5412683.0, rms=2.670 (0.000%) rms = 2.64, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=5446473.5, rms=2.636 (0.000%) positioning took 0.4 minutes writing curvature file /HD4/Subjects/subj_23_1.long.s23_base/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /HD4/Subjects/subj_23_1.long.s23_base/surf/rh.area.pial vertex spacing 1.01 +- 0.42 (0.02-->6.50) (max @ vno 131526 --> 131517) face area 0.41 +- 0.30 (0.00-->10.05) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 147659 vertices processed 25000 of 147659 vertices processed 50000 of 147659 vertices processed 75000 of 147659 vertices processed 100000 of 147659 vertices processed 125000 of 147659 vertices processed 0 of 147659 vertices processed 25000 of 147659 vertices processed 50000 of 147659 vertices processed 75000 of 147659 vertices processed 100000 of 147659 vertices processed 125000 of 147659 vertices processed thickness calculation complete, 940:1092 truncations. 32623 vertices at 0 distance 104198 vertices at 1 distance 91754 vertices at 2 distance 36912 vertices at 3 distance 11602 vertices at 4 distance 3474 vertices at 5 distance 966 vertices at 6 distance 330 vertices at 7 distance 101 vertices at 8 distance 79 vertices at 9 distance 47 vertices at 10 distance 37 vertices at 11 distance 35 vertices at 12 distance 24 vertices at 13 distance 20 vertices at 14 distance 19 vertices at 15 distance 7 vertices at 16 distance 4 vertices at 17 distance 14 vertices at 18 distance 16 vertices at 19 distance 10 vertices at 20 distance writing curvature file /HD4/Subjects/subj_23_1.long.s23_base/surf/rh.thickness positioning took 7.2 minutes #-------------------------------------------- #@# Surf Volume rh Tue Oct 17 00:29:25 EDT 2017 /HD4/Subjects/subj_23_1.long.s23_base/surf mris_calc -o rh.area.mid rh.area add rh.area.pial Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.area.mid rh.area.mid div 2 Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.volume rh.area.mid mul rh.thickness WARNING: # of slices=-59 in header - assuming 124... read_signa(/HD4/Subjects/subj_23_1.long.s23_base/surf/I.001): could not open file No such file or directory mris_calc: Sorry, but I seem to have encountered an error. While checking on input filetype sizes, I found a size mismatch, i.e. len(input1)!=len(input2) Linux localhost.localdomain 3.10.0-327.3.1.el7.x86_64 #1 SMP Wed Dec 9 14:09:15 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux recon-all -s subj_23_1.long.s23_base exited with ERRORS at Tue Oct 17 00:29:26 EDT 2017 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting